0s autopkgtest [03:43:31]: starting date and time: 2025-10-29 03:43:31+0000
  0s autopkgtest [03:43:31]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [03:43:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eu0wv_0v/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/5.34-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-1.secgroup --name adt-resolute-amd64-trinityrnaseq-20251029-034330-juju-7f2275-prod-proposed-migration-environment-15-f22ab099-9096-4f12-a13e-e43075ba6578 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  3s Creating nova instance adt-resolute-amd64-trinityrnaseq-20251029-034330-juju-7f2275-prod-proposed-migration-environment-15-f22ab099-9096-4f12-a13e-e43075ba6578 from image adt/ubuntu-resolute-amd64-server-20251028.img (UUID 28aec2b7-3bf0-42f3-9f6e-cd514d583c29)...
 27s autopkgtest [03:43:58]: testbed dpkg architecture: amd64
 27s autopkgtest [03:43:58]: testbed apt version: 3.1.8ubuntu1
 28s autopkgtest [03:43:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 28s autopkgtest [03:43:59]: testbed release detected to be: None
 28s autopkgtest [03:43:59]: updating testbed package index (apt update)
 29s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB]
 29s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 29s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 29s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 29s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.0 kB]
 29s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3625 kB]
 29s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [203 kB]
 29s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B]
 29s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [179 kB]
 29s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [279 kB]
 29s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5160 B]
 30s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [4212 B]
 30s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.6 kB]
 30s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B]
 30s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [2497 kB]
 30s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [1103 kB]
 30s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [65.9 kB]
 30s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [19.6 kB]
 30s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [46.9 kB]
 30s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1792 B]
 31s Fetched 8221 kB in 2s (4496 kB/s)
 32s Reading package lists...
 32s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 32s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 32s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 32s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 33s Reading package lists...
 33s Reading package lists...
 33s Building dependency tree...
 33s Reading state information...
 33s Calculating upgrade...
 33s The following packages will be upgraded:
 33s   apt cloud-init cloud-init-base libapt-pkg7.0 libefiboot1t64 libefivar1t64
 33s   python3-blinker python3-lazr.uri
 33s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 33s Need to get 3371 kB of archives.
 33s After this operation, 140 kB of additional disk space will be used.
 33s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.11 [1148 kB]
 34s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.11 [1468 kB]
 34s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB]
 34s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B]
 34s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libefivar1t64 amd64 39-2 [61.0 kB]
 34s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libefiboot1t64 amd64 39-2 [41.7 kB]
 34s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-blinker all 1.9.0-2 [10.8 kB]
 34s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lazr.uri all 1.0.6-7 [13.8 kB]
 34s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 34s Fetched 3371 kB in 1s (5960 kB/s)
 34s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 78529 files and directories currently installed.)
 34s Preparing to unpack .../0-libapt-pkg7.0_3.1.11_amd64.deb ...
 34s Unpacking libapt-pkg7.0:amd64 (3.1.11) over (3.1.8ubuntu1) ...
 34s Preparing to unpack .../1-apt_3.1.11_amd64.deb ...
 34s Unpacking apt (3.1.11) over (3.1.8ubuntu1) ...
 34s Preparing to unpack .../2-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ...
 34s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ...
 34s Preparing to unpack .../3-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ...
 34s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ...
 34s Preparing to unpack .../4-libefivar1t64_39-2_amd64.deb ...
 34s Unpacking libefivar1t64:amd64 (39-2) over (38-3.1build1) ...
 35s Preparing to unpack .../5-libefiboot1t64_39-2_amd64.deb ...
 35s Unpacking libefiboot1t64:amd64 (39-2) over (38-3.1build1) ...
 35s Preparing to unpack .../6-python3-blinker_1.9.0-2_all.deb ...
 35s Unpacking python3-blinker (1.9.0-2) over (1.9.0-1) ...
 35s Preparing to unpack .../7-python3-lazr.uri_1.0.6-7_all.deb ...
 35s Unpacking python3-lazr.uri (1.0.6-7) over (1.0.6-6) ...
 35s Setting up libefivar1t64:amd64 (39-2) ...
 35s Setting up python3-lazr.uri (1.0.6-7) ...
 35s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ...
 35s Encountered debconf setting for cloud-init-base/datasources.
 36s Setting up libefiboot1t64:amd64 (39-2) ...
 36s Setting up libapt-pkg7.0:amd64 (3.1.11) ...
 36s Setting up python3-blinker (1.9.0-2) ...
 36s Setting up apt (3.1.11) ...
 36s Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ...
 36s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ...
 36s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ...
 36s Processing triggers for man-db (2.13.1-1) ...
 37s Processing triggers for libc-bin (2.42-0ubuntu3) ...
 37s autopkgtest [03:44:08]: upgrading testbed (apt dist-upgrade and autopurge)
 38s Reading package lists...
 38s Building dependency tree...
 38s Reading state information...
 38s Calculating upgrade...
 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 38s Reading package lists...
 39s Building dependency tree...
 39s Reading state information...
 39s Solving dependencies...
 39s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 39s autopkgtest [03:44:10]: rebooting testbed after setup commands that affected boot
 53s autopkgtest [03:44:24]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025
 55s autopkgtest [03:44:26]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq
 67s Get:1 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (dsc) [2605 B]
 67s Get:2 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (tar) [305 MB]
 67s Get:3 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (diff) [38.9 kB]
 67s gpgv: Signature made Wed Aug 21 22:00:38 2024 UTC
 67s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
 67s gpgv: Can't check signature: No public key
 67s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.2+dfsg-1.dsc: no acceptable signature found
 71s autopkgtest [03:44:41]: testing package trinityrnaseq version 2.15.2+dfsg-1
 71s autopkgtest [03:44:42]: build not needed
 87s autopkgtest [03:44:58]: test run-tests: preparing testbed
 87s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s Solving dependencies...
 88s The following NEW packages will be installed:
 88s   adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2
 88s   ca-certificates-java dconf-gsettings-backend dconf-service default-jre
 88s   default-jre-headless fontconfig fontconfig-config fonts-dejavu-core
 88s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
 88s   fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2 jaligner
 88s   java-common javascript-common jellyfish junit4 kallisto libapache-pom-java
 88s   libasan8 libasound2-data libasound2t64 libatinject-jsr330-api-java
 88s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
 88s   libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java
 88s   libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0
 88s   libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.88-dev
 88s   libcairo-gobject2 libcairo2 libclone-perl libcolord2
 88s   libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java
 88s   libcommons-collections4-java libcommons-compress-java libcommons-io-java
 88s   libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java
 88s   libcommons-math3-java libcommons-parent-java libcups2t64 libdatrie1
 88s   libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-intel1 libencode-locale-perl
 88s   libepoxy0 liberror-prone-java libezmorph-java libfile-listing-perl
 88s   libfontconfig1 libfreemarker-java libgatk-native-bindings-java libgbm1
 88s   libgcc-15-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java
 88s   libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglvnd0
 88s   libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3
 88s   libgtk-3-0t64 libgtk-3-common libguava-java libhamcrest-java libharfbuzz0b
 88s   libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64
 88s   libhtscodecs2 libhtsjdk-java libhttp-cookies-perl libhttp-date-perl
 88s   libhttp-message-perl libhttp-negotiate-perl libhttpclient-java
 88s   libhttpcore-java libhwasan0 libhwloc15 libice6 libicu76 libio-html-perl
 88s   libio-socket-ssl-perl libitm1 libjaxen-java libjbig0 libjbzip2-java
 88s   libjellyfish-2.0-2 libjoptsimple-java libjpeg-turbo8 libjpeg8
 88s   libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js
 88s   libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js
 88s   libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js
 88s   libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js
 88s   libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore
 88s   libjson-java libjsr305-java libjung-free-java liblapack3 liblcms2-2 liblerc4
 88s   liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0
 88s   liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16
 88s   libmbedtls21 libmbedx509-7 libmongodb-java libncbi-ngs3 libncbi-vdb3
 88s   libnet-http-perl libnet-ssleay-perl libngs-java libngs-jni libnspr4 libnss3
 88s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
 88s   libpaper2 libpciaccess0 libpcsclite1 libpicard-java libpixman-1-0
 88s   libprotobuf32t64 libquadmath0 librhino-java libsharpyuv0 libslf4j-java
 88s   libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libstaden-read14t64
 88s   libstdc++-15-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6
 88s   libthai-data libthai0 libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl
 88s   libtsan2 libubsan1 liburi-perl libvulkan1 libwayland-client0
 88s   libwayland-cursor0 libwayland-egl1 libwebp7 libwww-perl
 88s   libwww-robotrules-perl libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-present0
 88s   libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0
 88s   libxcomposite1 libxcursor1 libxdamage1 libxerces2-java libxfixes3 libxft2
 88s   libxi6 libxinerama1 libxml-commons-external-java
 88s   libxml-commons-resolver1.1-java libxom-java libxrandr2 libxrender1
 88s   libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 mesa-libgallium
 88s   ncbi-blast+ ncbi-data ncbi-vdb-data node-bootstrap-sass node-html5shiv
 88s   node-normalize.css openjdk-21-jre openjdk-21-jre-headless pandoc pandoc-data
 88s   parafly perl-openssl-defaults python3-hisat2 python3-htseq python3-numpy
 88s   python3-numpy-dev python3-pysam r-base-core r-bioc-annotate
 88s   r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics
 88s   r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings
 88s   r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger
 88s   r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter
 88s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
 88s   r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq
 88s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
 88s   r-bioc-qvalue r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
 88s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
 88s   r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils
 88s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-argparse r-cran-askpass
 88s   r-cran-backports r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-bit
 88s   r-cran-bit64 r-cran-bitops r-cran-blob r-cran-broom r-cran-bslib
 88s   r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli r-cran-clipr
 88s   r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-commonmark
 88s   r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table
 88s   r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dtplyr
 88s   r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
 88s   r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython
 88s   r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
 88s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
 88s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
 88s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
 88s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
 88s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
 88s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
 88s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
 88s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
 88s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
 88s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
 88s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
 88s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
 88s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
 88s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
 88s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
 88s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
 88s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
 88s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
 88s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
 88s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
 88s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
 88s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
 88s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
 88s   subread trimmomatic trinityrnaseq trinityrnaseq-examples unzip x11-common
 88s   xdg-utils zip zlib1g-dev
 88s 0 upgraded, 454 newly installed, 0 to remove and 0 not upgraded.
 88s Need to get 896 MB of archives.
 88s After this operation, 2178 MB of additional disk space will be used.
 88s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB]
 88s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB]
 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB]
 88s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB]
 88s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB]
 88s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf2.0-common all 2.44.4+dfsg-1 [8584 B]
 88s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB]
 88s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 88s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB]
 88s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 88s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
 88s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
 88s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
 88s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
 88s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf-2.0-0 amd64 2.44.4+dfsg-1 [153 kB]
 88s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 gtk-update-icon-cache amd64 4.20.2+ds-1 [54.6 kB]
 88s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB]
 88s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 adwaita-icon-theme all 49.0-1 [581 kB]
 88s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 at-spi2-common all 2.57.1-1 [9432 B]
 88s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB]
 88s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5ubuntu2 [289 kB]
 88s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5ubuntu2 [324 kB]
 88s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-thread1.83.0 amd64 1.83.0-5ubuntu2 [278 kB]
 88s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libprotobuf32t64 amd64 3.21.12-14build1 [955 kB]
 88s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 berkeley-express amd64 1.5.3+dfsg-3build6 [214 kB]
 88s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118 [11.6 kB]
 88s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libdconf1 amd64 0.49.0-1 [40.2 kB]
 88s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-service amd64 0.49.0-1 [27.7 kB]
 88s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-gsettings-backend amd64 0.49.0-1 [22.2 kB]
 88s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76 [6852 B]
 88s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 88s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libnspr4 amd64 2:4.36-1ubuntu2 [118 kB]
 89s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnss3 amd64 2:3.114-1 [1483 kB]
 89s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.3.3-1 [24.0 kB]
 89s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.9+10-1 [46.5 MB]
 89s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
 89s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libatk1.0-0t64 amd64 2.57.1-1 [56.3 kB]
 89s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB]
 89s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libatspi2.0-0t64 amd64 2.57.1-1 [85.3 kB]
 89s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libatk-bridge2.0-0t64 amd64 2.57.1-1 [66.7 kB]
 89s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 89s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 89s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB]
 89s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB]
 89s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
 89s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB]
 89s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B]
 89s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
 89s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB]
 89s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-gobject2 amd64 1.18.4-1build1 [128 kB]
 89s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolord2 amd64 1.4.7-3build1 [149 kB]
 89s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common-data amd64 0.8-16ubuntu3 [31.1 kB]
 89s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common3 amd64 0.8-16ubuntu3 [25.3 kB]
 89s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-client3 amd64 0.8-16ubuntu3 [28.8 kB]
 89s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libcups2t64 amd64 2.4.12-0ubuntu3 [272 kB]
 89s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB]
 89s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 89s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB]
 89s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB]
 89s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
 89s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.13-4 [19.3 kB]
 89s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
 89s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB]
 89s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [52.5 kB]
 89s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [29.0 kB]
 89s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-client0 amd64 1.24.0-1build1 [29.6 kB]
 89s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-cursor0 amd64 1.24.0-1build1 [11.1 kB]
 89s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-egl1 amd64 1.24.0-1build1 [6474 B]
 89s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B]
 89s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB]
 89s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB]
 89s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B]
 89s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B]
 89s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB]
 89s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-3-common all 3.24.50-1ubuntu2 [1425 kB]
 89s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-3-0t64 amd64 3.24.50-1ubuntu2 [3263 kB]
 89s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libglvnd0 amd64 1.7.0-1build2 [65.1 kB]
 89s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libx11-xcb1 amd64 2:1.8.12-1build1 [8044 B]
 89s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-dri3-0 amd64 1.17.0-2build1 [8036 B]
 89s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-glx0 amd64 1.17.0-2build1 [27.6 kB]
 89s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-present0 amd64 1.17.0-2build1 [6446 B]
 89s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xfixes0 amd64 1.17.0-2build1 [11.1 kB]
 89s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B]
 89s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.127-1ubuntu1 [23.6 kB]
 89s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB]
 89s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-intel1 amd64 2.4.127-1ubuntu1 [69.2 kB]
 89s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-randr0 amd64 1.17.0-2build1 [19.7 kB]
 89s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-sync1 amd64 1.17.0-2build1 [10.1 kB]
 89s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B]
 89s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 mesa-libgallium amd64 25.2.3-1ubuntu1 [11.1 MB]
 90s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libgbm1 amd64 25.2.3-1ubuntu1 [34.0 kB]
 90s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libvulkan1 amd64 1.4.321.0-1 [154 kB]
 90s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1-mesa-dri amd64 25.2.3-1ubuntu1 [36.9 kB]
 90s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx-mesa0 amd64 25.2.3-1ubuntu1 [110 kB]
 90s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx0 amd64 1.7.0-1build2 [40.3 kB]
 90s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1 amd64 1.7.0-1build2 [101 kB]
 90s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2-data all 1.2.14-1ubuntu1 [21.2 kB]
 90s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2t64 amd64 1.2.14-1ubuntu1 [407 kB]
 90s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libgif7 amd64 5.2.2-1ubuntu2 [36.0 kB]
 90s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
 90s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB]
 90s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre amd64 21.0.9+10-1 [225 kB]
 90s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre amd64 2:1.21-76 [918 B]
 90s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
 90s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
 90s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
 90s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 hisat2 amd64 2.2.1-5 [3889 kB]
 90s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 jaligner all 1.0+dfsg-11 [136 kB]
 90s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1 [4828 B]
 90s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB]
 90s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB]
 90s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjellyfish-2.0-2 amd64 2.3.1-4build2 [70.1 kB]
 90s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 jellyfish amd64 2.3.1-4build2 [773 kB]
 90s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhamcrest-java all 2.2-2 [117 kB]
 90s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 junit4 all 4.13.2-5 [348 kB]
 90s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 kallisto amd64 0.48.0+dfsg-4build1 [273 kB]
 90s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2 [5874 B]
 90s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-5ubuntu1 [3071 kB]
 90s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B]
 90s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
 90s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-lang3-java all 3.17.0-1 [603 kB]
 90s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfreemarker-java all 2.3.32-2.1 [1517 kB]
 90s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB]
 90s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjoptsimple-java all 5.0.4-7 [73.2 kB]
 90s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-codec-java all 1.18.0-1 [303 kB]
 90s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB]
 90s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB]
 90s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB]
 90s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB]
 90s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB]
 90s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 libslf4j-java all 1.7.32-2 [141 kB]
 90s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB]
 90s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
 90s Get:134 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB]
 90s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-5ubuntu1 [29.3 kB]
 90s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-5ubuntu1 [1360 kB]
 90s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-5ubuntu1 [2757 kB]
 91s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-5ubuntu1 [1210 kB]
 91s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-5ubuntu1 [1685 kB]
 91s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-5ubuntu1 [153 kB]
 91s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-5ubuntu1 [2863 kB]
 91s Get:142 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-5ubuntu1 [2573 kB]
 91s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.88-dev amd64 1.88.0-1.4ubuntu2 [11.3 MB]
 91s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.88.0.0ubuntu1 [4542 B]
 91s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-5ubuntu2 [261 kB]
 91s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libclone-perl amd64 0.47-1 [10.7 kB]
 91s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-collections3-java all 3.2.2-3 [526 kB]
 91s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-beanutils-java all 1.10.1-1.1 [224 kB]
 91s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-collections4-java all 4.4-2 [670 kB]
 91s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-io-java all 2.19.0-1 [491 kB]
 91s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB]
 91s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB]
 91s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-math3-java all 3.6.1-4 [2029 kB]
 91s Get:154 http://ftpmaster.internal/ubuntu resolute/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB]
 91s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjsr305-java all 0.1~+svn49-12 [27.0 kB]
 91s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
 91s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
 91s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 libezmorph-java all 1.0.6-4 [76.0 kB]
 91s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB]
 91s Get:160 http://ftpmaster.internal/ubuntu resolute/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB]
 91s Get:161 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB]
 91s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B]
 91s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB]
 91s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjaxen-java all 1.1.6-5 [213 kB]
 91s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
 91s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB]
 91s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxerces2-java all 2.12.2-1 [1430 kB]
 91s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxom-java all 1.3.9-1 [174 kB]
 91s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjson-java all 3.1.0+dfsg-2 [141 kB]
 91s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB]
 91s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB]
 91s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB]
 91s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB]
 92s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1376 kB]
 92s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-ngs3 amd64 3.2.1+dfsg-4ubuntu5 [152 kB]
 92s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 libngs-jni amd64 3.2.1+dfsg-4ubuntu5 [4814 B]
 92s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 libngs-java amd64 3.2.1+dfsg-4ubuntu5 [91.1 kB]
 92s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 librhino-java all 1.7.15-1 [1354 kB]
 92s Get:179 http://ftpmaster.internal/ubuntu resolute/main amd64 libsnappy1v5 amd64 1.2.2-1 [30.9 kB]
 92s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsnappy-jni amd64 1.1.10.7-1 [6786 B]
 92s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsnappy-java all 1.1.10.7-1 [83.6 kB]
 92s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1829 kB]
 92s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB]
 92s Get:184 http://ftpmaster.internal/ubuntu resolute/main amd64 libhtml-tagset-perl all 3.24-1 [14.1 kB]
 92s Get:185 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 liburi-perl all 5.34-2 [100 kB]
 92s Get:186 http://ftpmaster.internal/ubuntu resolute/main amd64 libhtml-parser-perl amd64 3.83-1build1 [86.2 kB]
 92s Get:187 http://ftpmaster.internal/ubuntu resolute/main amd64 libhtml-tree-perl all 5.07-3 [200 kB]
 92s Get:188 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-html-perl all 1.004-3 [15.9 kB]
 92s Get:189 http://ftpmaster.internal/ubuntu resolute/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB]
 92s Get:190 http://ftpmaster.internal/ubuntu resolute/main amd64 libhttp-message-perl all 7.00-2ubuntu1 [75.9 kB]
 92s Get:191 http://ftpmaster.internal/ubuntu resolute/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB]
 92s Get:192 http://ftpmaster.internal/ubuntu resolute/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB]
 92s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB]
 92s Get:194 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
 92s Get:195 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu76 amd64 76.1-4ubuntu2 [11.2 MB]
 92s Get:196 http://ftpmaster.internal/ubuntu resolute/main amd64 perl-openssl-defaults amd64 7build3 [6626 B]
 92s Get:197 http://ftpmaster.internal/ubuntu resolute/main amd64 libnet-ssleay-perl amd64 1.94-3 [318 kB]
 92s Get:198 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-socket-ssl-perl all 2.089-1 [200 kB]
 92s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
 92s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
 92s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
 92s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4 [132 kB]
 92s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
 92s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
 92s Get:205 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
 92s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
 92s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
 92s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
 92s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
 92s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
 92s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
 92s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
 92s Get:213 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
 92s Get:214 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB]
 92s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjung-free-java all 2.1.1-3 [1478 kB]
 92s Get:216 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
 92s Get:217 http://ftpmaster.internal/ubuntu resolute/main amd64 libnet-http-perl all 6.23-1 [22.3 kB]
 92s Get:218 http://ftpmaster.internal/ubuntu resolute/main amd64 libtry-tiny-perl all 0.32-1 [21.2 kB]
 92s Get:219 http://ftpmaster.internal/ubuntu resolute/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB]
 92s Get:220 http://ftpmaster.internal/ubuntu resolute/main amd64 libwww-perl all 6.78-1 [139 kB]
 92s Get:221 http://ftpmaster.internal/ubuntu resolute/main amd64 liblwp-protocol-https-perl all 6.14-1 [9040 B]
 92s Get:222 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
 92s Get:223 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
 92s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpicard-java all 3.3.0+dfsg-2 [1765 kB]
 92s Get:225 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB]
 92s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 libstaden-read14t64 amd64 1.15.0-1.1build2 [251 kB]
 92s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtbbbind-2-5 amd64 2022.1.0-1 [14.7 kB]
 92s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtbbmalloc2 amd64 2022.1.0-1 [53.7 kB]
 92s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtbb12 amd64 2022.1.0-1 [93.5 kB]
 92s Get:230 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB]
 92s Get:231 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
 92s Get:232 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
 93s Get:233 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
 93s Get:234 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
 93s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB]
 93s Get:236 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB]
 94s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
 94s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
 94s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB]
 94s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
 94s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
 95s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 parafly amd64 0.1.0-5 [17.4 kB]
 95s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-hisat2 all 2.2.1-5 [12.7 kB]
 95s Get:244 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.0+ds-1build2 [4551 kB]
 95s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-htseq amd64 2.0.9+dfsg-1build3 [484 kB]
 95s Get:246 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB]
 95s Get:247 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB]
 95s Get:248 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
 95s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.1-1 [28.9 MB]
 96s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
 96s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
 96s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
 97s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
 97s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB]
 97s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
 97s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB]
 97s Get:257 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
 97s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
 97s Get:259 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
 97s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
 97s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
 97s Get:262 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
 97s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
 97s Get:264 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
 97s Get:265 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
 97s Get:266 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
 97s Get:267 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
 97s Get:268 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB]
 97s Get:269 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
 97s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 6.2.1+dfsg-1ubuntu1 [197 kB]
 97s Get:271 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
 97s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
 97s Get:273 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
 97s Get:274 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
 97s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
 97s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
 97s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
 97s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
 97s Get:279 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
 97s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
 97s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
 97s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
 97s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
 98s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
 98s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
 98s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
 99s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB]
 99s Get:288 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
100s Get:289 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.18-1build1 [1745 kB]
100s Get:290 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
100s Get:291 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB]
100s Get:292 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB]
100s Get:293 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
100s Get:294 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
100s Get:295 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
100s Get:296 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB]
100s Get:297 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
100s Get:298 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
100s Get:299 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
100s Get:300 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB]
101s Get:301 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB]
101s Get:302 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB]
101s Get:303 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
101s Get:304 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
101s Get:305 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbplyr all 2.5.0+dfsg-1 [1233 kB]
101s Get:306 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB]
101s Get:307 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocfilecache all 2.14.0+dfsg-2 [300 kB]
101s Get:308 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB]
101s Get:309 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
101s Get:310 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
101s Get:311 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
101s Get:312 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
101s Get:313 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
101s Get:314 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB]
101s Get:315 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
101s Get:316 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
101s Get:317 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB]
101s Get:318 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
101s Get:319 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
101s Get:320 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB]
101s Get:321 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr2 all 1.1.1-1 [752 kB]
101s Get:322 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB]
101s Get:323 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml2 amd64 1.4.0-1ubuntu1 [329 kB]
101s Get:324 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biomart all 2.62.1+dfsg-1 [444 kB]
101s Get:325 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB]
101s Get:326 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB]
102s Get:327 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
102s Get:328 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
102s Get:329 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB]
102s Get:330 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
102s Get:331 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1391 kB]
102s Get:332 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
102s Get:333 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
102s Get:334 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
103s Get:335 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-locfit amd64 1.5-9.12-1 [552 kB]
103s Get:336 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
103s Get:337 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
103s Get:338 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
103s Get:339 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB]
103s Get:340 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-3-1 [3414 kB]
103s Get:341 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
103s Get:342 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
103s Get:343 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB]
103s Get:344 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB]
103s Get:345 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
103s Get:346 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB]
104s Get:347 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.3.0-1 [603 kB]
104s Get:348 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
104s Get:349 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.21-1 [99.3 kB]
104s Get:350 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
104s Get:351 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
104s Get:352 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 14.6.0-1-1 [862 kB]
105s Get:353 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-deseq2 amd64 1.46.0+dfsg-2 [1250 kB]
105s Get:354 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hwriter all 1.3.2.1-1 [106 kB]
105s Get:355 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
105s Get:356 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB]
105s Get:357 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB]
105s Get:358 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
105s Get:359 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-geneplotter all 1.84.0+dfsg-2 [1508 kB]
106s Get:360 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB]
106s Get:361 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genefilter amd64 1.88.0-2 [1243 kB]
106s Get:362 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-dexseq all 1.52.0+dfsg-2 [453 kB]
106s Get:363 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-limma amd64 3.62.2+dfsg-1 [1969 kB]
107s Get:364 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-edger amd64 4.4.2+dfsg-1 [1120 kB]
107s Get:365 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB]
107s Get:366 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
107s Get:367 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB]
107s Get:368 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
107s Get:369 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
107s Get:370 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rtracklayer amd64 1.66.0-3 [5225 kB]
107s Get:371 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB]
107s Get:372 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-txdbmaker all 1.2.1+ds-2 [875 kB]
107s Get:373 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genelendatabase all 1.42.0-3 [100 MB]
114s Get:374 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-go.db all 3.20.0-2 [16.5 MB]
114s Get:375 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-biasedurn amd64 2.0.12-1 [290 kB]
114s Get:376 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-goseq all 1.58.0-2 [1911 kB]
114s Get:377 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
114s Get:378 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB]
114s Get:379 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-qvalue all 2.38.0-2 [2811 kB]
115s Get:380 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-findpython all 1.0.9-1 [25.3 kB]
115s Get:381 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-argparse all 2.2.5+dfsg-1 [143 kB]
115s Get:382 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB]
115s Get:383 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB]
115s Get:384 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB]
115s Get:385 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
115s Get:386 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
115s Get:387 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
115s Get:388 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
115s Get:389 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
115s Get:390 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
115s Get:391 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
115s Get:392 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
115s Get:393 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB]
115s Get:394 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB]
115s Get:395 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB]
115s Get:396 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cluster amd64 2.1.8.1-1 [579 kB]
115s Get:397 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
115s Get:398 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB]
115s Get:399 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB]
115s Get:400 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dtplyr all 1.3.1-1 [364 kB]
115s Get:401 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB]
115s Get:402 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB]
115s Get:403 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastcluster amd64 1.3.0-1build1 [193 kB]
115s Get:404 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
115s Get:405 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB]
115s Get:406 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gargle all 1.5.2-1 [737 kB]
115s Get:407 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB]
115s Get:408 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB]
115s Get:409 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-googledrive all 2.1.1-3 [1238 kB]
115s Get:410 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ids all 1.0.1-2 [124 kB]
115s Get:411 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB]
115s Get:412 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-googlesheets4 all 1.1.1-1 [520 kB]
115s Get:413 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gridextra all 2.3-3build1 [1024 kB]
115s Get:414 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-goplot all 1.0.2-2 [2427 kB]
115s Get:415 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tzdb amd64 0.5.0-1 [538 kB]
115s Get:416 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB]
115s Get:417 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB]
115s Get:418 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-haven amd64 2.5.5-1 [364 kB]
115s Get:419 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.51+dfsg-1 [574 kB]
116s Get:420 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
116s Get:421 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
116s Get:422 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
116s Get:423 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
116s Get:424 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kernsmooth amd64 2.23-26-1 [94.5 kB]
116s Get:425 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
116s Get:426 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.50+dfsg-1 [840 kB]
116s Get:427 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timechange amd64 0.3.0-2 [201 kB]
116s Get:428 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB]
116s Get:429 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB]
116s Get:430 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-systemfonts amd64 1.2.1-1 [347 kB]
116s Get:431 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-textshaping amd64 0.3.7-2 [95.5 kB]
116s Get:432 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ragg amd64 1.3.3-1 [510 kB]
116s Get:433 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-readxl amd64 1.4.5-1 [361 kB]
116s Get:434 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.56-1 [148 kB]
116s Get:435 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1 [101 kB]
116s Get:436 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
116s Get:437 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
116s Get:438 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
117s Get:439 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.29+dfsg-1 [1501 kB]
117s Get:440 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rstudioapi all 0.17.1-1 [299 kB]
117s Get:441 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reprex all 2.1.1-1 [468 kB]
117s Get:442 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-selectr all 0.4-2-2build1 [416 kB]
117s Get:443 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rvest all 1.0.5-1 [301 kB]
117s Get:444 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyverse all 2.0.0+dfsg-2 [85.2 kB]
117s Get:445 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie amd64 1.3.1-3 [1562 kB]
117s Get:446 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB]
117s Get:447 http://ftpmaster.internal/ubuntu resolute/universe amd64 rsem amd64 1.3.3+dfsg-3build1 [36.1 MB]
118s Get:448 http://ftpmaster.internal/ubuntu resolute/universe amd64 salmon amd64 1.10.2+ds1-1build2 [3308 kB]
118s Get:449 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.21-1 [655 kB]
118s Get:450 http://ftpmaster.internal/ubuntu resolute/universe amd64 subread amd64 2.0.8+dfsg-1 [549 kB]
118s Get:451 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB]
118s Get:452 http://ftpmaster.internal/ubuntu resolute/universe amd64 trimmomatic all 0.39+dfsg-2 [758 kB]
118s Get:453 http://ftpmaster.internal/ubuntu resolute/universe amd64 trinityrnaseq amd64 2.15.2+dfsg-1 [1779 kB]
118s Get:454 http://ftpmaster.internal/ubuntu resolute/universe amd64 trinityrnaseq-examples amd64 2.15.2+dfsg-1 [299 MB]
132s Preconfiguring packages ...
132s Fetched 896 MB in 44s (20.4 MB/s)
132s Selecting previously unselected package python3-numpy-dev:amd64.
132s (Reading database ... 
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(Reading database ... 78531 files and directories currently installed.)
132s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ...
132s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ...
132s Selecting previously unselected package libblas3:amd64.
132s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ...
132s Unpacking libblas3:amd64 (3.12.1-6build1) ...
132s Selecting previously unselected package libgfortran5:amd64.
132s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_amd64.deb ...
132s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ...
132s Selecting previously unselected package liblapack3:amd64.
132s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ...
132s Unpacking liblapack3:amd64 (3.12.1-6build1) ...
132s Selecting previously unselected package python3-numpy.
132s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ...
132s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ...
132s Selecting previously unselected package libgdk-pixbuf2.0-common.
132s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.44.4+dfsg-1_all.deb ...
132s Unpacking libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ...
132s Selecting previously unselected package libjpeg-turbo8:amd64.
132s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ...
132s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ...
132s Selecting previously unselected package libjpeg8:amd64.
132s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ...
132s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
132s Selecting previously unselected package libdeflate0:amd64.
132s Preparing to unpack .../008-libdeflate0_1.23-2_amd64.deb ...
132s Unpacking libdeflate0:amd64 (1.23-2) ...
132s Selecting previously unselected package libjbig0:amd64.
132s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
132s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
132s Selecting previously unselected package liblerc4:amd64.
132s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ...
132s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
132s Selecting previously unselected package libsharpyuv0:amd64.
132s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_amd64.deb ...
132s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ...
132s Selecting previously unselected package libwebp7:amd64.
132s Preparing to unpack .../012-libwebp7_1.5.0-0.1_amd64.deb ...
132s Unpacking libwebp7:amd64 (1.5.0-0.1) ...
132s Selecting previously unselected package libtiff6:amd64.
132s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_amd64.deb ...
132s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ...
132s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64.
132s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.44.4+dfsg-1_amd64.deb ...
132s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.44.4+dfsg-1) ...
132s Selecting previously unselected package gtk-update-icon-cache.
132s Preparing to unpack .../015-gtk-update-icon-cache_4.20.2+ds-1_amd64.deb ...
133s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
133s 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.
133s Unpacking gtk-update-icon-cache (4.20.2+ds-1) ...
133s Selecting previously unselected package hicolor-icon-theme.
133s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ...
133s Unpacking hicolor-icon-theme (0.18-2) ...
133s Selecting previously unselected package adwaita-icon-theme.
133s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ...
133s Unpacking adwaita-icon-theme (49.0-1) ...
133s Selecting previously unselected package at-spi2-common.
133s Preparing to unpack .../018-at-spi2-common_2.57.1-1_all.deb ...
133s Unpacking at-spi2-common (2.57.1-1) ...
133s Selecting previously unselected package libbamtools2.5.2:amd64.
133s Preparing to unpack .../019-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ...
133s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ...
133s Selecting previously unselected package libboost-filesystem1.83.0:amd64.
133s Preparing to unpack .../020-libboost-filesystem1.83.0_1.83.0-5ubuntu2_amd64.deb ...
133s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-5ubuntu2) ...
133s Selecting previously unselected package libboost-program-options1.83.0:amd64.
133s Preparing to unpack .../021-libboost-program-options1.83.0_1.83.0-5ubuntu2_amd64.deb ...
133s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-5ubuntu2) ...
133s Selecting previously unselected package libboost-thread1.83.0:amd64.
133s Preparing to unpack .../022-libboost-thread1.83.0_1.83.0-5ubuntu2_amd64.deb ...
133s Unpacking libboost-thread1.83.0:amd64 (1.83.0-5ubuntu2) ...
133s Selecting previously unselected package libprotobuf32t64:amd64.
133s Preparing to unpack .../023-libprotobuf32t64_3.21.12-14build1_amd64.deb ...
133s Unpacking libprotobuf32t64:amd64 (3.21.12-14build1) ...
133s Selecting previously unselected package berkeley-express.
133s Preparing to unpack .../024-berkeley-express_1.5.3+dfsg-3build6_amd64.deb ...
133s Unpacking berkeley-express (1.5.3+dfsg-3build6) ...
133s Selecting previously unselected package ca-certificates-java.
133s Preparing to unpack .../025-ca-certificates-java_20240118_all.deb ...
133s Unpacking ca-certificates-java (20240118) ...
133s Selecting previously unselected package libdconf1:amd64.
133s Preparing to unpack .../026-libdconf1_0.49.0-1_amd64.deb ...
133s Unpacking libdconf1:amd64 (0.49.0-1) ...
133s Selecting previously unselected package dconf-service.
133s Preparing to unpack .../027-dconf-service_0.49.0-1_amd64.deb ...
133s Unpacking dconf-service (0.49.0-1) ...
133s Selecting previously unselected package dconf-gsettings-backend:amd64.
133s Preparing to unpack .../028-dconf-gsettings-backend_0.49.0-1_amd64.deb ...
133s Unpacking dconf-gsettings-backend:amd64 (0.49.0-1) ...
133s Selecting previously unselected package java-common.
133s Preparing to unpack .../029-java-common_0.76_all.deb ...
133s Unpacking java-common (0.76) ...
133s Selecting previously unselected package liblcms2-2:amd64.
133s Preparing to unpack .../030-liblcms2-2_2.16-2_amd64.deb ...
133s Unpacking liblcms2-2:amd64 (2.16-2) ...
133s Selecting previously unselected package libnspr4:amd64.
133s Preparing to unpack .../031-libnspr4_2%3a4.36-1ubuntu2_amd64.deb ...
133s Unpacking libnspr4:amd64 (2:4.36-1ubuntu2) ...
133s Selecting previously unselected package libnss3:amd64.
133s Preparing to unpack .../032-libnss3_2%3a3.114-1_amd64.deb ...
133s Unpacking libnss3:amd64 (2:3.114-1) ...
133s Selecting previously unselected package libpcsclite1:amd64.
133s Preparing to unpack .../033-libpcsclite1_2.3.3-1_amd64.deb ...
133s Unpacking libpcsclite1:amd64 (2.3.3-1) ...
133s Selecting previously unselected package openjdk-21-jre-headless:amd64.
133s Preparing to unpack .../034-openjdk-21-jre-headless_21.0.9+10-1_amd64.deb ...
133s Unpacking openjdk-21-jre-headless:amd64 (21.0.9+10-1) ...
133s Selecting previously unselected package default-jre-headless.
133s Preparing to unpack .../035-default-jre-headless_2%3a1.21-76_amd64.deb ...
133s Unpacking default-jre-headless (2:1.21-76) ...
133s Selecting previously unselected package libatk1.0-0t64:amd64.
133s Preparing to unpack .../036-libatk1.0-0t64_2.57.1-1_amd64.deb ...
133s Unpacking libatk1.0-0t64:amd64 (2.57.1-1) ...
133s Selecting previously unselected package libxi6:amd64.
133s Preparing to unpack .../037-libxi6_2%3a1.8.2-1_amd64.deb ...
133s Unpacking libxi6:amd64 (2:1.8.2-1) ...
133s Selecting previously unselected package libatspi2.0-0t64:amd64.
133s Preparing to unpack .../038-libatspi2.0-0t64_2.57.1-1_amd64.deb ...
133s Unpacking libatspi2.0-0t64:amd64 (2.57.1-1) ...
133s Selecting previously unselected package libatk-bridge2.0-0t64:amd64.
133s Preparing to unpack .../039-libatk-bridge2.0-0t64_2.57.1-1_amd64.deb ...
133s Unpacking libatk-bridge2.0-0t64:amd64 (2.57.1-1) ...
133s Selecting previously unselected package fonts-dejavu-mono.
133s Preparing to unpack .../040-fonts-dejavu-mono_2.37-8_all.deb ...
133s Unpacking fonts-dejavu-mono (2.37-8) ...
133s Selecting previously unselected package fonts-dejavu-core.
133s Preparing to unpack .../041-fonts-dejavu-core_2.37-8_all.deb ...
133s Unpacking fonts-dejavu-core (2.37-8) ...
133s Selecting previously unselected package fontconfig-config.
133s Preparing to unpack .../042-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ...
133s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ...
133s Selecting previously unselected package libfontconfig1:amd64.
133s Preparing to unpack .../043-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ...
133s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ...
133s Selecting previously unselected package libpixman-1-0:amd64.
134s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_amd64.deb ...
134s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
134s Selecting previously unselected package libxcb-render0:amd64.
134s Preparing to unpack .../045-libxcb-render0_1.17.0-2build1_amd64.deb ...
134s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ...
134s Selecting previously unselected package libxcb-shm0:amd64.
134s Preparing to unpack .../046-libxcb-shm0_1.17.0-2build1_amd64.deb ...
134s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ...
134s Selecting previously unselected package libxrender1:amd64.
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136s Selecting previously unselected package libcommons-math3-java.
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136s Selecting previously unselected package libencode-locale-perl.
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136s Selecting previously unselected package libjsr305-java.
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136s Selecting previously unselected package liberror-prone-java.
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136s Selecting previously unselected package libezmorph-java.
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136s Selecting previously unselected package libtimedate-perl.
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136s Selecting previously unselected package libhttp-date-perl.
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136s Selecting previously unselected package libgatk-native-bindings-java.
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136s Selecting previously unselected package libxml-commons-external-java.
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136s Selecting previously unselected package libxerces2-java.
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136s Selecting previously unselected package libmbedcrypto16:amd64.
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136s Selecting previously unselected package libmbedtls21:amd64.
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136s Selecting previously unselected package ncbi-vdb-data.
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136s Selecting previously unselected package libncbi-vdb3:amd64.
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136s Selecting previously unselected package libncbi-ngs3:amd64.
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136s Selecting previously unselected package libngs-jni:amd64.
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136s Selecting previously unselected package libngs-java:amd64.
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136s Selecting previously unselected package librhino-java.
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136s Selecting previously unselected package libsnappy1v5:amd64.
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136s Selecting previously unselected package libsnappy-jni.
136s Preparing to unpack .../179-libsnappy-jni_1.1.10.7-1_amd64.deb ...
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136s Selecting previously unselected package libsnappy-java.
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136s Selecting previously unselected package libhtsjdk-java.
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136s Selecting previously unselected package libgkl-java.
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136s Selecting previously unselected package libhtml-tagset-perl.
136s Preparing to unpack .../183-libhtml-tagset-perl_3.24-1_all.deb ...
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136s Selecting previously unselected package liburi-perl.
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136s Selecting previously unselected package libhtml-parser-perl:amd64.
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136s Selecting previously unselected package libhtml-tree-perl.
136s Preparing to unpack .../186-libhtml-tree-perl_5.07-3_all.deb ...
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136s Selecting previously unselected package libio-html-perl.
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136s Selecting previously unselected package liblwp-mediatypes-perl.
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136s Selecting previously unselected package libhttp-message-perl.
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136s Selecting previously unselected package libhttp-cookies-perl.
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136s Selecting previously unselected package libhttp-negotiate-perl.
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136s Selecting previously unselected package libhwloc15:amd64.
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136s Selecting previously unselected package libice6:amd64.
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136s Selecting previously unselected package libicu76:amd64.
136s Preparing to unpack .../194-libicu76_76.1-4ubuntu2_amd64.deb ...
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137s Selecting previously unselected package perl-openssl-defaults:amd64.
137s Preparing to unpack .../195-perl-openssl-defaults_7build3_amd64.deb ...
137s Unpacking perl-openssl-defaults:amd64 (7build3) ...
137s Selecting previously unselected package libnet-ssleay-perl:amd64.
137s Preparing to unpack .../196-libnet-ssleay-perl_1.94-3_amd64.deb ...
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137s Selecting previously unselected package libio-socket-ssl-perl.
137s Preparing to unpack .../197-libio-socket-ssl-perl_2.089-1_all.deb ...
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137s Selecting previously unselected package libjs-bootstrap.
137s Preparing to unpack .../198-libjs-bootstrap_3.4.1+dfsg-6_all.deb ...
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137s Selecting previously unselected package libjs-popper.js.
137s Preparing to unpack .../199-libjs-popper.js_1.16.1+ds-6_all.deb ...
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137s Selecting previously unselected package libjs-bootstrap4.
137s Preparing to unpack .../200-libjs-bootstrap4_4.6.2+dfsg-1_all.deb ...
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137s Selecting previously unselected package libjs-d3.
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137s Selecting previously unselected package libjs-es5-shim.
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137s Selecting previously unselected package libjs-highlight.js.
137s Preparing to unpack .../203-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
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137s Selecting previously unselected package libjs-jquery.
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137s Selecting previously unselected package libjs-jquery-datatables.
137s Preparing to unpack .../205-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
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137s Selecting previously unselected package libjs-sifter.js.
137s Preparing to unpack .../206-libjs-sifter.js_0.6.0+dfsg-3_all.deb ...
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137s Selecting previously unselected package libjs-microplugin.js.
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137s Selecting previously unselected package libjs-jquery-selectize.js.
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137s Selecting previously unselected package libjs-jquery-ui.
137s Preparing to unpack .../209-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
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137s Selecting previously unselected package libjs-json.
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137s Selecting previously unselected package libjs-prettify.
137s Preparing to unpack .../211-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ...
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137s Selecting previously unselected package libjs-underscore.
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137s Selecting previously unselected package libjs-sphinxdoc.
137s Preparing to unpack .../213-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ...
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137s Selecting previously unselected package libjung-free-java.
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137s Selecting previously unselected package liblua5.4-0:amd64.
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137s Selecting previously unselected package libnet-http-perl.
137s Preparing to unpack .../216-libnet-http-perl_6.23-1_all.deb ...
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137s Selecting previously unselected package libtry-tiny-perl.
137s Preparing to unpack .../217-libtry-tiny-perl_0.32-1_all.deb ...
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137s Selecting previously unselected package libwww-robotrules-perl.
137s Preparing to unpack .../218-libwww-robotrules-perl_6.02-1_all.deb ...
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137s Selecting previously unselected package libwww-perl.
137s Preparing to unpack .../219-libwww-perl_6.78-1_all.deb ...
137s Unpacking libwww-perl (6.78-1) ...
137s Selecting previously unselected package liblwp-protocol-https-perl.
137s Preparing to unpack .../220-liblwp-protocol-https-perl_6.14-1_all.deb ...
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137s Selecting previously unselected package libpaper2:amd64.
137s Preparing to unpack .../221-libpaper2_2.2.5-0.3_amd64.deb ...
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137s Selecting previously unselected package libpaper-utils.
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137s Selecting previously unselected package libpicard-java.
137s Preparing to unpack .../223-libpicard-java_3.3.0+dfsg-2_all.deb ...
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137s Selecting previously unselected package libsm6:amd64.
137s Preparing to unpack .../224-libsm6_2%3a1.2.6-1_amd64.deb ...
137s Unpacking libsm6:amd64 (2:1.2.6-1) ...
137s Selecting previously unselected package libstaden-read14t64:amd64.
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137s Selecting previously unselected package libtbbbind-2-5:amd64.
137s Preparing to unpack .../226-libtbbbind-2-5_2022.1.0-1_amd64.deb ...
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137s Selecting previously unselected package libtbbmalloc2:amd64.
137s Preparing to unpack .../227-libtbbmalloc2_2022.1.0-1_amd64.deb ...
137s Unpacking libtbbmalloc2:amd64 (2022.1.0-1) ...
137s Selecting previously unselected package libtbb12:amd64.
137s Preparing to unpack .../228-libtbb12_2022.1.0-1_amd64.deb ...
137s Unpacking libtbb12:amd64 (2022.1.0-1) ...
137s Selecting previously unselected package libtcl8.6:amd64.
137s Preparing to unpack .../229-libtcl8.6_8.6.17+dfsg-1_amd64.deb ...
137s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ...
137s Selecting previously unselected package libxft2:amd64.
137s Preparing to unpack .../230-libxft2_2.3.6-1build1_amd64.deb ...
137s Unpacking libxft2:amd64 (2.3.6-1build1) ...
137s Selecting previously unselected package libxss1:amd64.
137s Preparing to unpack .../231-libxss1_1%3a1.2.3-1build3_amd64.deb ...
137s Unpacking libxss1:amd64 (1:1.2.3-1build3) ...
137s Selecting previously unselected package libtk8.6:amd64.
137s Preparing to unpack .../232-libtk8.6_8.6.17-1_amd64.deb ...
137s Unpacking libtk8.6:amd64 (8.6.17-1) ...
137s Selecting previously unselected package libxt6t64:amd64.
137s Preparing to unpack .../233-libxt6t64_1%3a1.2.1-1.3_amd64.deb ...
137s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ...
137s Selecting previously unselected package ncbi-data.
137s Preparing to unpack .../234-ncbi-data_6.1.20170106+dfsg2-6_all.deb ...
137s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ...
137s Selecting previously unselected package ncbi-blast+.
137s Preparing to unpack .../235-ncbi-blast+_2.16.0+ds-7_amd64.deb ...
137s Unpacking ncbi-blast+ (2.16.0+ds-7) ...
138s Selecting previously unselected package node-bootstrap-sass.
138s Preparing to unpack .../236-node-bootstrap-sass_3.4.3-2_all.deb ...
138s Unpacking node-bootstrap-sass (3.4.3-2) ...
138s Selecting previously unselected package node-html5shiv.
138s Preparing to unpack .../237-node-html5shiv_3.7.3+dfsg-5_all.deb ...
138s Unpacking node-html5shiv (3.7.3+dfsg-5) ...
138s Selecting previously unselected package node-normalize.css.
138s Preparing to unpack .../238-node-normalize.css_8.0.1-5_all.deb ...
138s Unpacking node-normalize.css (8.0.1-5) ...
138s Selecting previously unselected package pandoc-data.
138s Preparing to unpack .../239-pandoc-data_3.1.11.1-3build1_all.deb ...
138s Unpacking pandoc-data (3.1.11.1-3build1) ...
138s Selecting previously unselected package pandoc.
138s Preparing to unpack .../240-pandoc_3.1.11.1+ds-4_amd64.deb ...
138s Unpacking pandoc (3.1.11.1+ds-4) ...
138s Selecting previously unselected package parafly.
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138s Unpacking parafly (0.1.0-5) ...
138s Selecting previously unselected package python3-hisat2.
138s Preparing to unpack .../242-python3-hisat2_2.2.1-5_all.deb ...
138s Unpacking python3-hisat2 (2.2.1-5) ...
138s Selecting previously unselected package python3-pysam.
138s Preparing to unpack .../243-python3-pysam_0.23.0+ds-1build2_amd64.deb ...
138s Unpacking python3-pysam (0.23.0+ds-1build2) ...
138s Selecting previously unselected package python3-htseq.
138s Preparing to unpack .../244-python3-htseq_2.0.9+dfsg-1build3_amd64.deb ...
138s Unpacking python3-htseq (2.0.9+dfsg-1build3) ...
138s Selecting previously unselected package zip.
138s Preparing to unpack .../245-zip_3.0-15ubuntu2_amd64.deb ...
138s Unpacking zip (3.0-15ubuntu2) ...
138s Selecting previously unselected package unzip.
138s Preparing to unpack .../246-unzip_6.0-28ubuntu7_amd64.deb ...
138s Unpacking unzip (6.0-28ubuntu7) ...
138s Selecting previously unselected package xdg-utils.
138s Preparing to unpack .../247-xdg-utils_1.2.1-2ubuntu1_all.deb ...
138s Unpacking xdg-utils (1.2.1-2ubuntu1) ...
138s Selecting previously unselected package r-base-core.
138s Preparing to unpack .../248-r-base-core_4.5.1-1_amd64.deb ...
138s Unpacking r-base-core (4.5.1-1) ...
138s Selecting previously unselected package r-bioc-biocgenerics.
138s Preparing to unpack .../249-r-bioc-biocgenerics_0.52.0-2_all.deb ...
138s Unpacking r-bioc-biocgenerics (0.52.0-2) ...
138s Selecting previously unselected package r-bioc-biobase.
138s Preparing to unpack .../250-r-bioc-biobase_2.66.0-2_amd64.deb ...
138s Unpacking r-bioc-biobase (2.66.0-2) ...
138s Selecting previously unselected package r-bioc-s4vectors.
138s Preparing to unpack .../251-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ...
138s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ...
138s Selecting previously unselected package r-bioc-iranges.
138s Preparing to unpack .../252-r-bioc-iranges_2.40.1-3_amd64.deb ...
138s Unpacking r-bioc-iranges (2.40.1-3) ...
138s Selecting previously unselected package r-cran-dbi.
138s Preparing to unpack .../253-r-cran-dbi_1.2.3-1_all.deb ...
138s Unpacking r-cran-dbi (1.2.3-1) ...
138s Selecting previously unselected package r-cran-bit.
138s Preparing to unpack .../254-r-cran-bit_4.6.0+dfsg-1_amd64.deb ...
138s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
138s Selecting previously unselected package r-cran-bit64.
138s Preparing to unpack .../255-r-cran-bit64_4.6.0-1-4_amd64.deb ...
138s Unpacking r-cran-bit64 (4.6.0-1-4) ...
138s Selecting previously unselected package r-cran-rlang.
138s Preparing to unpack .../256-r-cran-rlang_1.1.5-3_amd64.deb ...
138s Unpacking r-cran-rlang (1.1.5-3) ...
139s Selecting previously unselected package r-cran-cli.
139s Preparing to unpack .../257-r-cran-cli_3.6.4-1_amd64.deb ...
139s Unpacking r-cran-cli (3.6.4-1) ...
139s Selecting previously unselected package r-cran-glue.
139s Preparing to unpack .../258-r-cran-glue_1.8.0-1_amd64.deb ...
139s Unpacking r-cran-glue (1.8.0-1) ...
139s Selecting previously unselected package r-cran-lifecycle.
139s Preparing to unpack .../259-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
139s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
139s Selecting previously unselected package r-cran-vctrs.
139s Preparing to unpack .../260-r-cran-vctrs_0.6.5-1_amd64.deb ...
139s Unpacking r-cran-vctrs (0.6.5-1) ...
139s Selecting previously unselected package r-cran-blob.
139s Preparing to unpack .../261-r-cran-blob_1.2.4-1_all.deb ...
139s Unpacking r-cran-blob (1.2.4-1) ...
139s Selecting previously unselected package r-cran-fastmap.
139s Preparing to unpack .../262-r-cran-fastmap_1.2.0-1_amd64.deb ...
139s Unpacking r-cran-fastmap (1.2.0-1) ...
139s Selecting previously unselected package r-cran-cachem.
139s Preparing to unpack .../263-r-cran-cachem_1.1.0-1_amd64.deb ...
139s Unpacking r-cran-cachem (1.1.0-1) ...
139s Selecting previously unselected package r-cran-memoise.
139s Preparing to unpack .../264-r-cran-memoise_2.0.1-1_all.deb ...
139s Unpacking r-cran-memoise (2.0.1-1) ...
139s Selecting previously unselected package r-cran-pkgconfig.
139s Preparing to unpack .../265-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
139s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
139s Selecting previously unselected package r-cran-plogr.
139s Preparing to unpack .../266-r-cran-plogr_0.2.0-3build1_all.deb ...
139s Unpacking r-cran-plogr (0.2.0-3build1) ...
139s Selecting previously unselected package r-cran-cpp11.
139s Preparing to unpack .../267-r-cran-cpp11_0.5.2-1_all.deb ...
139s Unpacking r-cran-cpp11 (0.5.2-1) ...
139s Selecting previously unselected package r-cran-rsqlite.
139s Preparing to unpack .../268-r-cran-rsqlite_2.3.9-1_amd64.deb ...
139s Unpacking r-cran-rsqlite (2.3.9-1) ...
139s Selecting previously unselected package r-cran-curl.
139s Preparing to unpack .../269-r-cran-curl_6.2.1+dfsg-1ubuntu1_amd64.deb ...
139s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
139s Selecting previously unselected package r-cran-jsonlite.
139s Preparing to unpack .../270-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ...
139s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ...
139s Selecting previously unselected package r-cran-mime.
139s Preparing to unpack .../271-r-cran-mime_0.12-2_amd64.deb ...
139s Unpacking r-cran-mime (0.12-2) ...
139s Selecting previously unselected package r-cran-sys.
139s Preparing to unpack .../272-r-cran-sys_3.4.3-1_amd64.deb ...
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139s Selecting previously unselected package r-cran-askpass.
139s Preparing to unpack .../273-r-cran-askpass_1.2.1-1_amd64.deb ...
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139s Selecting previously unselected package r-cran-openssl.
139s Preparing to unpack .../274-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ...
139s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
139s Selecting previously unselected package r-cran-r6.
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139s Selecting previously unselected package r-cran-httr.
139s Preparing to unpack .../276-r-cran-httr_1.4.7+dfsg-1_all.deb ...
139s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
139s Selecting previously unselected package r-cran-png.
139s Preparing to unpack .../277-r-cran-png_0.1-8-1build2_amd64.deb ...
139s Unpacking r-cran-png (0.1-8-1build2) ...
139s Selecting previously unselected package zlib1g-dev:amd64.
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139s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ...
139s Selecting previously unselected package r-bioc-zlibbioc.
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139s Selecting previously unselected package r-bioc-xvector.
139s Preparing to unpack .../280-r-bioc-xvector_0.46.0-2_amd64.deb ...
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139s Selecting previously unselected package r-bioc-ucsc.utils.
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139s Selecting previously unselected package r-bioc-genomeinfodbdata.
139s Preparing to unpack .../282-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ...
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139s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
139s Selecting previously unselected package r-cran-crayon.
139s Preparing to unpack .../284-r-cran-crayon_1.5.3-1_all.deb ...
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139s Selecting previously unselected package r-bioc-biostrings.
139s Preparing to unpack .../285-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ...
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139s Selecting previously unselected package r-bioc-keggrest.
139s Preparing to unpack .../286-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ...
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139s Selecting previously unselected package r-bioc-annotationdbi.
139s Preparing to unpack .../287-r-bioc-annotationdbi_1.68.0-2_all.deb ...
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139s Selecting previously unselected package r-cran-xml.
139s Preparing to unpack .../288-r-cran-xml_3.99-0.18-1build1_amd64.deb ...
139s Unpacking r-cran-xml (3.99-0.18-1build1) ...
139s Selecting previously unselected package r-cran-xtable.
139s Preparing to unpack .../289-r-cran-xtable_1%3a1.8-4-2_all.deb ...
139s Unpacking r-cran-xtable (1:1.8-4-2) ...
139s Selecting previously unselected package r-bioc-annotate.
139s Preparing to unpack .../290-r-bioc-annotate_1.84.0+dfsg-2_all.deb ...
139s Unpacking r-bioc-annotate (1.84.0+dfsg-2) ...
139s Selecting previously unselected package r-cran-generics.
139s Preparing to unpack .../291-r-cran-generics_0.1.3-1_all.deb ...
139s Unpacking r-cran-generics (0.1.3-1) ...
139s Selecting previously unselected package r-cran-magrittr.
139s Preparing to unpack .../292-r-cran-magrittr_2.0.3-1_amd64.deb ...
139s Unpacking r-cran-magrittr (2.0.3-1) ...
139s Selecting previously unselected package r-cran-utf8.
139s Preparing to unpack .../293-r-cran-utf8_1.2.4-1_amd64.deb ...
139s Unpacking r-cran-utf8 (1.2.4-1) ...
139s Selecting previously unselected package r-cran-pillar.
139s Preparing to unpack .../294-r-cran-pillar_1.10.1+dfsg-1_all.deb ...
139s Unpacking r-cran-pillar (1.10.1+dfsg-1) ...
139s Selecting previously unselected package r-cran-fansi.
139s Preparing to unpack .../295-r-cran-fansi_1.0.6-2_amd64.deb ...
139s Unpacking r-cran-fansi (1.0.6-2) ...
139s Selecting previously unselected package r-cran-tibble.
139s Preparing to unpack .../296-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ...
139s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
139s Selecting previously unselected package r-cran-withr.
139s Preparing to unpack .../297-r-cran-withr_3.0.2+dfsg-1_all.deb ...
139s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
139s Selecting previously unselected package r-cran-tidyselect.
139s Preparing to unpack .../298-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ...
139s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
139s Selecting previously unselected package r-cran-dplyr.
139s Preparing to unpack .../299-r-cran-dplyr_1.1.4-4_amd64.deb ...
139s Unpacking r-cran-dplyr (1.1.4-4) ...
139s Selecting previously unselected package r-cran-purrr.
139s Preparing to unpack .../300-r-cran-purrr_1.0.4-1_amd64.deb ...
139s Unpacking r-cran-purrr (1.0.4-1) ...
139s Selecting previously unselected package r-cran-stringi.
139s Preparing to unpack .../301-r-cran-stringi_1.8.4-1build1_amd64.deb ...
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139s Selecting previously unselected package r-cran-stringr.
139s Preparing to unpack .../302-r-cran-stringr_1.5.1-1_all.deb ...
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139s Selecting previously unselected package r-cran-tidyr.
139s Preparing to unpack .../303-r-cran-tidyr_1.3.1-1_amd64.deb ...
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139s Selecting previously unselected package r-cran-dbplyr.
139s Preparing to unpack .../304-r-cran-dbplyr_2.5.0+dfsg-1_all.deb ...
139s Unpacking r-cran-dbplyr (2.5.0+dfsg-1) ...
139s Selecting previously unselected package r-cran-filelock.
139s Preparing to unpack .../305-r-cran-filelock_1.0.3-1_amd64.deb ...
139s Unpacking r-cran-filelock (1.0.3-1) ...
139s Selecting previously unselected package r-bioc-biocfilecache.
139s Preparing to unpack .../306-r-bioc-biocfilecache_2.14.0+dfsg-2_all.deb ...
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139s Selecting previously unselected package r-bioc-biocio.
139s Preparing to unpack .../307-r-bioc-biocio_1.16.0+dfsg-2_all.deb ...
139s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ...
139s Selecting previously unselected package r-cran-formatr.
139s Preparing to unpack .../308-r-cran-formatr_1.14-2_all.deb ...
139s Unpacking r-cran-formatr (1.14-2) ...
139s Selecting previously unselected package r-cran-lambda.r.
139s Preparing to unpack .../309-r-cran-lambda.r_1.2.4-2build1_all.deb ...
139s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
139s Selecting previously unselected package r-cran-futile.options.
139s Preparing to unpack .../310-r-cran-futile.options_1.0.1-3build1_all.deb ...
139s Unpacking r-cran-futile.options (1.0.1-3build1) ...
139s Selecting previously unselected package r-cran-futile.logger.
139s Preparing to unpack .../311-r-cran-futile.logger_1.4.3-4build1_all.deb ...
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139s Selecting previously unselected package r-cran-snow.
139s Preparing to unpack .../312-r-cran-snow_1%3a0.4.4-2_all.deb ...
139s Unpacking r-cran-snow (1:0.4.4-2) ...
139s Selecting previously unselected package r-cran-codetools.
139s Preparing to unpack .../313-r-cran-codetools_0.2-20-1_all.deb ...
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139s Selecting previously unselected package r-cran-bh.
139s Preparing to unpack .../314-r-cran-bh_1.84.0-1_all.deb ...
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139s Selecting previously unselected package r-bioc-biocparallel.
140s Preparing to unpack .../315-r-bioc-biocparallel_1.40.0-2_amd64.deb ...
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140s Selecting previously unselected package r-cran-hms.
140s Preparing to unpack .../316-r-cran-hms_1.1.3-1_all.deb ...
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140s Selecting previously unselected package r-cran-prettyunits.
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140s Selecting previously unselected package r-cran-progress.
140s Preparing to unpack .../318-r-cran-progress_1.2.3-1_all.deb ...
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140s Selecting previously unselected package r-cran-rappdirs.
140s Preparing to unpack .../319-r-cran-rappdirs_0.3.3-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-httr2.
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140s Selecting previously unselected package r-cran-digest.
140s Preparing to unpack .../321-r-cran-digest_0.6.37-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-xml2.
140s Preparing to unpack .../322-r-cran-xml2_1.4.0-1ubuntu1_amd64.deb ...
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140s Selecting previously unselected package r-bioc-biomart.
140s Preparing to unpack .../323-r-bioc-biomart_2.62.1+dfsg-1_all.deb ...
140s Unpacking r-bioc-biomart (2.62.1+dfsg-1) ...
140s Selecting previously unselected package r-cran-lattice.
140s Preparing to unpack .../324-r-cran-lattice_0.22-7-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-matrix.
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140s Preparing to unpack .../326-r-cran-matrixstats_1.5.0-1_amd64.deb ...
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140s Selecting previously unselected package r-bioc-matrixgenerics.
140s Preparing to unpack .../327-r-bioc-matrixgenerics_1.18.1-1_all.deb ...
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140s Selecting previously unselected package r-cran-abind.
140s Preparing to unpack .../328-r-cran-abind_1.4-8-1_all.deb ...
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140s Selecting previously unselected package r-bioc-s4arrays.
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140s Selecting previously unselected package r-bioc-genomicranges.
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140s Selecting previously unselected package r-bioc-summarizedexperiment.
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140s Selecting previously unselected package r-cran-locfit.
140s Preparing to unpack .../334-r-cran-locfit_1.5-9.12-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-gtable.
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140s Selecting previously unselected package r-cran-isoband.
140s Preparing to unpack .../336-r-cran-isoband_0.2.7-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-mass.
140s Preparing to unpack .../337-r-cran-mass_7.3-65-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-nlme.
140s Preparing to unpack .../338-r-cran-nlme_3.1.168-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-mgcv.
140s Preparing to unpack .../339-r-cran-mgcv_1.9-3-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-farver.
140s Preparing to unpack .../340-r-cran-farver_2.1.2-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-labeling.
140s Preparing to unpack .../341-r-cran-labeling_0.4.3-1_all.deb ...
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140s Selecting previously unselected package r-cran-colorspace.
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140s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ...
140s Selecting previously unselected package r-cran-munsell.
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140s Unpacking r-cran-munsell (0.5.1-1) ...
140s Selecting previously unselected package r-cran-rcolorbrewer.
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140s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
140s Selecting previously unselected package r-cran-viridislite.
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140s Unpacking r-cran-viridislite (0.4.2-2) ...
140s Selecting previously unselected package r-cran-scales.
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140s Selecting previously unselected package r-cran-ggplot2.
140s Preparing to unpack .../347-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
140s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
140s Selecting previously unselected package r-cran-littler.
140s Preparing to unpack .../348-r-cran-littler_0.3.21-1_amd64.deb ...
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140s Selecting previously unselected package r-cran-pkgkitten.
140s Preparing to unpack .../349-r-cran-pkgkitten_0.2.4-1_all.deb ...
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140s Selecting previously unselected package r-cran-rcpp.
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140s Selecting previously unselected package r-cran-rcpparmadillo.
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140s Unpacking r-cran-rcpparmadillo (14.6.0-1-1) ...
140s Selecting previously unselected package r-bioc-deseq2.
140s Preparing to unpack .../352-r-bioc-deseq2_1.46.0+dfsg-2_amd64.deb ...
140s Unpacking r-bioc-deseq2 (1.46.0+dfsg-2) ...
140s Selecting previously unselected package r-cran-hwriter.
140s Preparing to unpack .../353-r-cran-hwriter_1.3.2.1-1_all.deb ...
140s Unpacking r-cran-hwriter (1.3.2.1-1) ...
140s Selecting previously unselected package r-cran-bitops.
140s Preparing to unpack .../354-r-cran-bitops_1.0-9-1_amd64.deb ...
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140s Selecting previously unselected package r-bioc-rhtslib.
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140s Selecting previously unselected package r-bioc-rsamtools.
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140s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ...
140s Selecting previously unselected package r-cran-statmod.
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140s Unpacking r-cran-statmod (1.5.0-1) ...
140s Selecting previously unselected package r-bioc-geneplotter.
140s Preparing to unpack .../358-r-bioc-geneplotter_1.84.0+dfsg-2_all.deb ...
140s Unpacking r-bioc-geneplotter (1.84.0+dfsg-2) ...
140s Selecting previously unselected package r-cran-survival.
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140s Selecting previously unselected package r-bioc-genefilter.
140s Preparing to unpack .../360-r-bioc-genefilter_1.88.0-2_amd64.deb ...
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140s Selecting previously unselected package r-bioc-dexseq.
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140s Selecting previously unselected package r-bioc-limma.
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140s Selecting previously unselected package r-bioc-edger.
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140s Selecting previously unselected package r-bioc-genomicalignments.
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140s Selecting previously unselected package r-cran-rcurl.
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140s Selecting previously unselected package r-cran-rjson.
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141s Selecting previously unselected package r-cran-yaml.
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141s Selecting previously unselected package r-cran-restfulr.
141s Preparing to unpack .../368-r-cran-restfulr_0.0.15-1_amd64.deb ...
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141s Selecting previously unselected package r-bioc-rtracklayer.
141s Preparing to unpack .../369-r-bioc-rtracklayer_1.66.0-3_amd64.deb ...
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141s Selecting previously unselected package r-bioc-genomicfeatures.
141s Preparing to unpack .../370-r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ...
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141s Selecting previously unselected package r-bioc-txdbmaker.
141s Preparing to unpack .../371-r-bioc-txdbmaker_1.2.1+ds-2_all.deb ...
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141s Selecting previously unselected package r-bioc-genelendatabase.
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141s Selecting previously unselected package r-bioc-go.db.
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141s Selecting previously unselected package r-cran-biasedurn.
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141s Selecting previously unselected package r-bioc-goseq.
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141s Selecting previously unselected package r-cran-plyr.
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141s Selecting previously unselected package r-cran-reshape2.
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141s Selecting previously unselected package r-bioc-qvalue.
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141s Selecting previously unselected package r-cran-findpython.
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141s Selecting previously unselected package r-cran-argparse.
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141s Selecting previously unselected package r-cran-base64enc.
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141s Selecting previously unselected package r-cran-broom.
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141s Selecting previously unselected package r-cran-htmltools.
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141s Selecting previously unselected package r-cran-jquerylib.
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141s Selecting previously unselected package r-cran-fs.
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141s Selecting previously unselected package r-cran-sass.
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141s Selecting previously unselected package r-cran-processx.
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141s Selecting previously unselected package r-cran-callr.
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141s Selecting previously unselected package r-cran-rematch.
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141s Selecting previously unselected package r-cran-cellranger.
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141s Selecting previously unselected package r-cran-clipr.
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141s Selecting previously unselected package r-cran-cluster.
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141s Selecting previously unselected package r-cran-commonmark.
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142s Selecting previously unselected package r-cran-conflicted.
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142s Selecting previously unselected package r-cran-data.table.
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142s Selecting previously unselected package r-cran-dtplyr.
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142s Selecting previously unselected package r-cran-ellipsis.
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142s Selecting previously unselected package r-cran-evaluate.
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142s Selecting previously unselected package r-cran-fastcluster.
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142s Selecting previously unselected package r-cran-fontawesome.
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142s Selecting previously unselected package r-cran-forcats.
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142s Selecting previously unselected package r-cran-gargle.
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142s Selecting previously unselected package r-cran-ggdendro.
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142s Selecting previously unselected package r-cran-uuid.
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142s Selecting previously unselected package r-cran-googledrive.
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142s Selecting previously unselected package r-cran-ids.
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142s Selecting previously unselected package r-cran-rematch2.
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142s Selecting previously unselected package r-cran-googlesheets4.
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142s Selecting previously unselected package r-cran-gridextra.
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142s Selecting previously unselected package r-cran-goplot.
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142s Selecting previously unselected package r-cran-tzdb.
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142s Selecting previously unselected package r-cran-vroom.
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142s Selecting previously unselected package r-cran-readr.
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142s Selecting previously unselected package r-cran-httpuv.
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142s Selecting previously unselected package r-cran-kernsmooth.
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142s Selecting previously unselected package libjs-mathjax.
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142s Selecting previously unselected package r-cran-knitr.
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142s Selecting previously unselected package r-cran-lubridate.
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143s Selecting previously unselected package r-cran-shiny.
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143s Selecting previously unselected package r-cran-reprex.
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143s Selecting previously unselected package r-cran-tidyverse.
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144s Setting up libhtscodecs2:amd64 (1.6.1-2) ...
144s Setting up libjs-json (0~20221030+~1.0.8-1) ...
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144s Setting up libboost-program-options1.83.0:amd64 (1.83.0-5ubuntu2) ...
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144s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
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148s Setting up r-base-core (4.5.1-1) ...
148s Creating config file /etc/R/Renviron with new version
148s Setting up r-cran-crayon (1.5.3-1) ...
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148s Setting up r-cran-sourcetools (0.1.7-1-1) ...
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148s Setting up r-cran-lattice (0.22-7-1) ...
148s Setting up r-cran-ps (1.9.0-1) ...
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148s Setting up r-cran-formatr (1.14-2) ...
148s Setting up r-cran-xml (3.99-0.18-1build1) ...
148s Setting up trinityrnaseq-examples (2.15.2+dfsg-1) ...
148s Setting up r-cran-viridislite (0.4.2-2) ...
148s Setting up r-cran-locfit (1.5-9.12-1) ...
148s Setting up r-cran-cluster (2.1.8.1-1) ...
148s Setting up rsem (1.3.3+dfsg-3build1) ...
148s Setting up r-cran-statmod (1.5.0-1) ...
148s Setting up r-cran-clipr (0.8.0-1) ...
148s Setting up r-cran-commonmark (1.9.5-1) ...
148s Setting up r-cran-rjson (0.2.23-1) ...
148s Setting up libngs-java:amd64 (3.2.1+dfsg-4ubuntu5) ...
148s Setting up r-cran-r6 (2.6.1-1) ...
148s Setting up r-cran-pkgkitten (0.2.4-1) ...
148s Setting up r-cran-fastcluster (1.3.0-1build1) ...
148s Setting up r-cran-magrittr (2.0.3-1) ...
148s Setting up r-cran-rappdirs (0.3.3-1) ...
148s Setting up r-cran-filelock (1.0.3-1) ...
148s Setting up libbarclay-java (5.0.0+dfsg-1) ...
148s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
148s Setting up r-cran-littler (0.3.21-1) ...
148s Setting up r-cran-bh (1.84.0-1) ...
148s Setting up r-cran-fs (1.6.5+dfsg-1) ...
148s Setting up r-cran-rcpp (1.1.0-1) ...
148s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
148s Setting up r-cran-codetools (0.2-20-1) ...
148s Setting up r-cran-rematch (2.0.0-1) ...
148s Setting up r-bioc-biocgenerics (0.52.0-2) ...
148s Setting up r-cran-rlang (1.1.5-3) ...
148s Setting up r-cran-matrixstats (1.5.0-1) ...
148s Setting up r-cran-findpython (1.0.9-1) ...
148s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
148s Setting up r-cran-uuid (1.2-1-1) ...
148s Setting up r-cran-xfun (0.51+dfsg-1) ...
148s Setting up r-cran-sys (3.4.3-1) ...
148s Setting up r-cran-plogr (0.2.0-3build1) ...
148s Setting up r-cran-withr (3.0.2+dfsg-1) ...
148s Setting up r-cran-backports (1.5.0-2) ...
148s Setting up r-cran-processx (3.8.6-1) ...
148s Setting up r-cran-mime (0.12-2) ...
148s Setting up r-cran-generics (0.1.3-1) ...
148s Setting up r-cran-base64enc (0.1-3-3) ...
148s Setting up r-cran-abind (1.4-8-1) ...
148s Setting up r-cran-digest (0.6.37-1) ...
148s Setting up r-cran-yaml (2.3.10-1) ...
148s Setting up r-cran-lambda.r (1.2.4-2build1) ...
148s Setting up r-cran-evaluate (1.0.3-1) ...
148s Setting up r-cran-dbi (1.2.3-1) ...
148s Setting up r-cran-highr (0.11+dfsg-1) ...
148s Setting up r-cran-prettyunits (1.2.0-1) ...
148s Setting up r-cran-fansi (1.0.6-2) ...
148s Setting up r-cran-mass (7.3-65-1) ...
148s Setting up r-cran-snow (1:0.4.4-2) ...
148s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
148s Setting up r-cran-glue (1.8.0-1) ...
148s Setting up r-cran-bit (4.6.0+dfsg-1) ...
148s Setting up r-cran-xtable (1:1.8-4-2) ...
148s Setting up r-cran-cli (3.6.4-1) ...
148s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
148s Setting up r-cran-bitops (1.0-9-1) ...
148s Setting up r-cran-bit64 (4.6.0-1-4) ...
148s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
148s Setting up r-cran-askpass (1.2.1-1) ...
148s Setting up r-cran-fastmap (1.2.0-1) ...
148s Setting up r-cran-png (0.1-8-1build2) ...
148s Setting up r-bioc-biobase (2.66.0-2) ...
148s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
148s Setting up r-cran-rstudioapi (0.17.1-1) ...
148s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
148s Setting up r-cran-utf8 (1.2.4-1) ...
148s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
148s Setting up r-cran-stringi (1.8.4-1build1) ...
148s Setting up r-cran-hwriter (1.3.2.1-1) ...
148s Setting up r-cran-cpp11 (0.5.2-1) ...
148s Setting up r-cran-plyr (1.8.9-1) ...
148s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
148s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
148s Setting up r-cran-isoband (0.2.7-1) ...
148s Setting up r-cran-futile.logger (1.4.3-4build1) ...
148s Setting up r-bioc-limma (3.62.2+dfsg-1) ...
148s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
148s Setting up r-cran-later (1.4.1+dfsg-1) ...
148s Setting up r-cran-matrix (1.7-3-1) ...
148s Setting up r-cran-htmltools (0.5.8.1-1) ...
148s Setting up r-cran-tinytex (0.56-1) ...
148s Setting up r-cran-kernsmooth (2.23-26-1) ...
148s Setting up r-cran-knitr (1.50+dfsg-1) ...
148s Setting up r-cran-mgcv (1.9-3-1) ...
148s Setting up r-cran-cachem (1.1.0-1) ...
148s Setting up r-cran-sass (0.4.9+dfsg-1) ...
148s Setting up r-cran-rcpparmadillo (14.6.0-1-1) ...
148s Setting up r-bioc-iranges (2.40.1-3) ...
148s Setting up r-cran-tzdb (0.5.0-1) ...
148s Setting up r-cran-argparse (2.2.5+dfsg-1) ...
148s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
148s Setting up r-cran-restfulr (0.0.15-1) ...
148s Setting up r-cran-vctrs (0.6.5-1) ...
148s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
148s Setting up r-cran-ellipsis (0.3.2-2) ...
148s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
148s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
148s Setting up r-cran-stringr (1.5.1-1) ...
148s Setting up r-bioc-biocparallel (1.40.0-2) ...
148s Setting up r-cran-callr (3.7.6-1) ...
148s Setting up r-cran-selectr (0.4-2-2build1) ...
148s Setting up r-bioc-edger (4.4.2+dfsg-1) ...
148s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
148s Setting up r-cran-xml2 (1.4.0-1ubuntu1) ...
148s Setting up r-cran-munsell (0.5.1-1) ...
148s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
148s Setting up r-cran-fontawesome (0.5.3-1) ...
148s Setting up r-cran-survival (3.8-3-1) ...
148s Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
148s Setting up r-cran-forcats (1.0.0-1) ...
148s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
148s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
148s Setting up r-cran-reshape2 (1.4.4-2build1) ...
148s Setting up r-cran-httr2 (1.1.1-1) ...
148s Setting up r-cran-systemfonts (1.2.1-1) ...
148s Setting up r-cran-ids (1.0.1-2) ...
148s Setting up r-cran-timechange (0.3.0-2) ...
148s Setting up r-cran-httr (1.4.7+dfsg-1) ...
148s Setting up r-cran-gridextra (2.3-3build1) ...
148s Setting up r-cran-hms (1.1.3-1) ...
148s Setting up r-cran-scales (1.3.0-1) ...
148s Setting up r-cran-memoise (2.0.1-1) ...
148s Setting up r-cran-promises (1.3.2+dfsg-1) ...
148s Setting up r-cran-purrr (1.0.4-1) ...
148s Setting up r-cran-blob (1.2.4-1) ...
148s Setting up r-bioc-xvector (0.46.0-2) ...
148s Setting up r-cran-dplyr (1.1.4-4) ...
148s Setting up r-cran-rsqlite (2.3.9-1) ...
148s Setting up r-cran-progress (1.2.3-1) ...
148s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
148s Setting up r-cran-gargle (1.5.2-1) ...
148s Setting up r-cran-vroom (1.6.5-1) ...
148s Setting up r-cran-conflicted (1.2.0-1.1) ...
148s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
148s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ...
148s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
148s Setting up r-cran-cellranger (1.1.0-3) ...
148s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
148s Setting up r-cran-rematch2 (2.1.2-2build1) ...
148s Setting up r-cran-textshaping (0.3.7-2) ...
148s Setting up r-cran-rvest (1.0.5-1) ...
148s Setting up r-cran-dtplyr (1.3.1-1) ...
148s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
148s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
148s Setting up r-cran-ragg (1.3.3-1) ...
148s Setting up r-cran-readr (2.1.5-1) ...
148s Setting up r-cran-tidyr (1.3.1-1) ...
148s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ...
148s Setting up r-cran-googledrive (2.1.1-3) ...
148s Setting up r-cran-googlesheets4 (1.1.1-1) ...
148s Setting up r-bioc-qvalue (2.38.0-2) ...
148s Setting up r-cran-dbplyr (2.5.0+dfsg-1) ...
148s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
148s Setting up r-cran-readxl (1.4.5-1) ...
148s Setting up r-bioc-biocfilecache (2.14.0+dfsg-2) ...
148s Setting up r-cran-haven (2.5.5-1) ...
148s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
148s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
148s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
148s Setting up r-cran-broom (1.0.7+dfsg-1) ...
148s Setting up r-cran-rmarkdown (2.29+dfsg-1) ...
148s Setting up r-cran-goplot (1.0.2-2) ...
148s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
148s Setting up r-cran-reprex (2.1.1-1) ...
148s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
148s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ...
148s Setting up r-bioc-deseq2 (1.46.0+dfsg-2) ...
148s Setting up r-bioc-annotationdbi (1.68.0-2) ...
148s Setting up r-bioc-go.db (3.20.0-2) ...
148s Setting up r-cran-modelr (0.1.11-1) ...
148s Setting up r-bioc-annotate (1.84.0+dfsg-2) ...
148s Setting up r-bioc-biomart (2.62.1+dfsg-1) ...
148s Setting up r-bioc-genefilter (1.88.0-2) ...
148s Setting up r-bioc-genomicalignments (1.42.0-2) ...
148s Setting up r-bioc-geneplotter (1.84.0+dfsg-2) ...
148s Setting up r-bioc-rtracklayer (1.66.0-3) ...
148s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
148s Setting up r-cran-tidyverse (2.0.0+dfsg-2) ...
148s Setting up r-bioc-dexseq (1.52.0+dfsg-2) ...
148s Setting up r-bioc-txdbmaker (1.2.1+ds-2) ...
148s Setting up r-bioc-genelendatabase (1.42.0-3) ...
148s Setting up r-bioc-goseq (1.58.0-2) ...
148s Setting up liblwp-protocol-https-perl (6.14-1) ...
148s Setting up liberror-prone-java (2.18.0-1) ...
148s Setting up libwww-perl (6.78-1) ...
148s Setting up libguava-java (32.0.1-1) ...
148s Setting up libjung-free-java (2.1.1-3) ...
148s Processing triggers for libglib2.0-0t64:amd64 (2.86.1-1) ...
148s Setting up libgtk-3-0t64:amd64 (3.24.50-1ubuntu2) ...
148s Processing triggers for install-info (7.1.1-1ubuntu1) ...
148s Processing triggers for libc-bin (2.42-0ubuntu3) ...
148s Processing triggers for man-db (2.13.1-1) ...
149s Processing triggers for ca-certificates-java (20240118) ...
149s Adding debian:ACCVRAIZ1.pem
149s Adding debian:AC_RAIZ_FNMT-RCM.pem
149s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
149s Adding debian:ANF_Secure_Server_Root_CA.pem
149s Adding debian:Actalis_Authentication_Root_CA.pem
149s Adding debian:AffirmTrust_Commercial.pem
149s Adding debian:AffirmTrust_Networking.pem
149s Adding debian:AffirmTrust_Premium.pem
149s Adding debian:AffirmTrust_Premium_ECC.pem
149s Adding debian:Amazon_Root_CA_1.pem
150s Adding debian:Amazon_Root_CA_2.pem
150s Adding debian:Amazon_Root_CA_3.pem
150s Adding debian:Amazon_Root_CA_4.pem
150s Adding debian:Atos_TrustedRoot_2011.pem
150s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
150s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
150s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
150s Adding debian:BJCA_Global_Root_CA1.pem
150s Adding debian:BJCA_Global_Root_CA2.pem
150s Adding debian:Baltimore_CyberTrust_Root.pem
150s Adding debian:Buypass_Class_2_Root_CA.pem
150s Adding debian:Buypass_Class_3_Root_CA.pem
150s Adding debian:CA_Disig_Root_R2.pem
150s Adding debian:CFCA_EV_ROOT.pem
150s Adding debian:COMODO_Certification_Authority.pem
150s Adding debian:COMODO_ECC_Certification_Authority.pem
150s Adding debian:COMODO_RSA_Certification_Authority.pem
150s Adding debian:Certainly_Root_E1.pem
150s Adding debian:Certainly_Root_R1.pem
150s Adding debian:Certigna.pem
150s Adding debian:Certigna_Root_CA.pem
150s Adding debian:Certum_EC-384_CA.pem
150s Adding debian:Certum_Trusted_Network_CA.pem
150s Adding debian:Certum_Trusted_Network_CA_2.pem
150s Adding debian:Certum_Trusted_Root_CA.pem
150s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
150s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
150s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
150s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
150s Adding debian:Comodo_AAA_Services_root.pem
150s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
150s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem
150s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
150s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem
150s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
150s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
150s Adding debian:DigiCert_Assured_ID_Root_CA.pem
150s Adding debian:DigiCert_Assured_ID_Root_G2.pem
150s Adding debian:DigiCert_Assured_ID_Root_G3.pem
150s Adding debian:DigiCert_Global_Root_CA.pem
150s Adding debian:DigiCert_Global_Root_G2.pem
150s Adding debian:DigiCert_Global_Root_G3.pem
150s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
150s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
150s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
150s Adding debian:DigiCert_Trusted_Root_G4.pem
150s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
150s Adding debian:Entrust_Root_Certification_Authority.pem
150s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
150s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
150s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
150s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
150s Adding debian:GLOBALTRUST_2020.pem
150s Adding debian:GTS_Root_R1.pem
150s Adding debian:GTS_Root_R2.pem
150s Adding debian:GTS_Root_R3.pem
150s Adding debian:GTS_Root_R4.pem
150s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
150s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
150s Adding debian:GlobalSign_Root_CA.pem
150s Adding debian:GlobalSign_Root_CA_-_R3.pem
150s Adding debian:GlobalSign_Root_CA_-_R6.pem
150s Adding debian:GlobalSign_Root_E46.pem
150s Adding debian:GlobalSign_Root_R46.pem
150s Adding debian:Go_Daddy_Class_2_CA.pem
150s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
150s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
150s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
150s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
150s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
150s Adding debian:HiPKI_Root_CA_-_G1.pem
150s Adding debian:Hongkong_Post_Root_CA_3.pem
150s Adding debian:ISRG_Root_X1.pem
150s Adding debian:ISRG_Root_X2.pem
150s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
150s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
150s Adding debian:Izenpe.com.pem
150s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
150s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
150s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
150s Adding debian:NAVER_Global_Root_Certification_Authority.pem
150s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
150s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
150s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
150s Adding debian:QuoVadis_Root_CA_1_G3.pem
150s Adding debian:QuoVadis_Root_CA_2.pem
150s Adding debian:QuoVadis_Root_CA_2_G3.pem
150s Adding debian:QuoVadis_Root_CA_3.pem
150s Adding debian:QuoVadis_Root_CA_3_G3.pem
150s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
150s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
150s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
150s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
150s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
150s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
150s Adding debian:SZAFIR_ROOT_CA2.pem
150s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
150s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
150s Adding debian:SecureSign_Root_CA12.pem
150s Adding debian:SecureSign_Root_CA14.pem
150s Adding debian:SecureSign_Root_CA15.pem
150s Adding debian:SecureTrust_CA.pem
150s Adding debian:Secure_Global_CA.pem
150s Adding debian:Security_Communication_ECC_RootCA1.pem
150s Adding debian:Security_Communication_RootCA2.pem
150s Adding debian:Starfield_Class_2_CA.pem
150s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
150s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
150s Adding debian:SwissSign_Gold_CA_-_G2.pem
150s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
150s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
150s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
150s Adding debian:TWCA_CYBER_Root_CA.pem
150s Adding debian:TWCA_Global_Root_CA.pem
150s Adding debian:TWCA_Root_Certification_Authority.pem
150s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
150s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
150s Adding debian:TeliaSonera_Root_CA_v1.pem
150s Adding debian:Telia_Root_CA_v2.pem
150s Adding debian:TrustAsia_Global_Root_CA_G3.pem
150s Adding debian:TrustAsia_Global_Root_CA_G4.pem
150s Adding debian:Trustwave_Global_Certification_Authority.pem
150s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
150s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
150s Adding debian:TunTrust_Root_CA.pem
150s Adding debian:UCA_Extended_Validation_Root.pem
150s Adding debian:UCA_Global_G2_Root.pem
150s Adding debian:USERTrust_ECC_Certification_Authority.pem
150s Adding debian:USERTrust_RSA_Certification_Authority.pem
150s Adding debian:XRamp_Global_CA_Root.pem
150s Adding debian:certSIGN_ROOT_CA.pem
150s Adding debian:certSIGN_Root_CA_G2.pem
150s Adding debian:e-Szigno_Root_CA_2017.pem
150s Adding debian:ePKI_Root_Certification_Authority.pem
150s Adding debian:emSign_ECC_Root_CA_-_C3.pem
150s Adding debian:emSign_ECC_Root_CA_-_G3.pem
150s Adding debian:emSign_Root_CA_-_C1.pem
150s Adding debian:emSign_Root_CA_-_G1.pem
150s Adding debian:vTrus_ECC_Root_CA.pem
150s Adding debian:vTrus_Root_CA.pem
150s done.
150s Setting up junit4 (4.13.2-5) ...
150s Setting up default-jre-headless (2:1.21-76) ...
150s Setting up jaligner (1.0+dfsg-11) ...
150s Setting up openjdk-21-jre:amd64 (21.0.9+10-1) ...
150s Setting up libjson-java (3.1.0+dfsg-2) ...
150s Setting up libhtsjdk-java (4.1.3+dfsg-2) ...
150s Setting up libgkl-java (0.8.11+dfsg-2build1) ...
150s Setting up default-jre (2:1.21-76) ...
150s Setting up libpicard-java (3.3.0+dfsg-2) ...
150s Setting up trimmomatic (0.39+dfsg-2) ...
150s Setting up trinityrnaseq (2.15.2+dfsg-1) ...
150s autopkgtest [03:46:01]: test run-tests: [-----------------------
151s cd test_Trinity_Assembly && make test_all
151s #!/bin/bash -ve
151s 
151s #######################################################
151s ##  Run Trinity to Generate Transcriptome Assemblies ##
151s #######################################################
151s 
151s if [ -z ${TRINITY_HOME} ]; then
151s     echo "Must set env var TRINITY_HOME"
151s     exit 1
151s fi
151s 
151s 
151s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
151s               --left reads.left.fq.gz \
151s               --right reads.right.fq.gz \
151s               --SS_lib_type RF \
151s               --CPU 1 \
151s               --no_cleanup
151s make[1]: Entering directory '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
151s ./runMe.sh
151s 
151s 
151s      ______  ____   ____  ____   ____  ______  __ __
151s     |      ||    \ |    ||    \ |    ||      ||  |  |
151s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
151s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
151s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
151s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
151s       |__|  |__|\_||____||__|__||____|  |__|  |____/
151s 
151s     Trinity-v2.15.2
151s 
151s 
151s 
151s Left read files: $VAR1 = [
151s           'reads.left.fq.gz'
151s         ];
151s Right read files: $VAR1 = [
151s           'reads.right.fq.gz'
151s         ];
151s Wednesday, October 29, 2025: 03:46:01	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir
151s Wednesday, October 29, 2025: 03:46:01	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis
151s 
151s 
151s ----------------------------------------------------------------------------------
151s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
151s ----------------------------------------------------------------------------------
151s 
151s ---------------------------------------------------------------
151s ------------ In silico Read Normalization ---------------------
151s -- (Removing Excess Reads Beyond 200 Coverage --
151s ---------------------------------------------------------------
151s 
151s # running normalization on reads: $VAR1 = [
151s           [
151s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
151s           ],
151s           [
151s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
151s           ]
151s         ];
151s 
151s 
151s Wednesday, October 29, 2025: 03:46:01	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
151s -prepping seqs
151s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
151s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
151s CMD finished (0 seconds)
151s CMD finished (0 seconds)
151s CMD: touch left.fa.ok
151s CMD finished (0 seconds)
151s CMD: touch right.fa.ok
151s CMD finished (0 seconds)
151s  Done converting input files. CMD: cat left.fa right.fa > both.fa
151s CMD finished (0 seconds)
151s CMD: touch both.fa.ok
151s CMD finished (0 seconds)
151s -kmer counting.
151s -------------------------------------------
151s ----------- Jellyfish  --------------------
151s -- (building a k-mer catalog from reads) --
151s -------------------------------------------
151s 
151s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
152s CMD finished (1 seconds)
152s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
152s CMD finished (0 seconds)
152s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
152s CMD finished (0 seconds)
152s CMD: touch jellyfish.K25.min2.kmers.fa.success
152s CMD finished (0 seconds)
152s -generating stats files
152s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
152s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
152s -reading Kmer occurrences...
152s -reading Kmer occurrences...
152s 
152s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
152s 
152s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
152s STATS_GENERATION_TIME: 1 seconds.
152s CMD finished (1 seconds)
152s STATS_GENERATION_TIME: 1 seconds.
152s CMD finished (1 seconds)
152s CMD: touch left.fa.K25.stats.ok
152s CMD finished (0 seconds)
152s CMD: touch right.fa.K25.stats.ok
152s CMD finished (0 seconds)
152s -sorting each stats file by read name.
152s 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
152s 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
153s CMD finished (0 seconds)
153s CMD finished (0 seconds)
153s CMD: touch left.fa.K25.stats.sort.ok
153s CMD finished (0 seconds)
153s CMD: touch right.fa.K25.stats.sort.ok
153s CMD finished (0 seconds)
153s -defining normalized reads
153s 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
153s -opening left.fa.K25.stats.sort
153s -opening right.fa.K25.stats.sort
153s -done opening files.
153s CMD finished (0 seconds)
153s CMD: touch pairs.K25.stats.ok
153s CMD finished (0 seconds)
153s 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
153s 30472 / 30575 = 99.66% reads selected during normalization.
153s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
153s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
153s CMD finished (0 seconds)
153s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
153s CMD finished (0 seconds)
153s -search and capture.
153s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
153s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
153s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
153s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
153s CMD: touch /tmp/autopkgtest.Uv0c5G/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
153s CMD finished (0 seconds)
153s CMD: touch /tmp/autopkgtest.Uv0c5G/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
153s CMD finished (0 seconds)
153s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
153s CMD finished (0 seconds)
153s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
153s CMD finished (0 seconds)
153s 
153s 
153s Normalization complete. See outputs: 
153s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
153s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
153s Wednesday, October 29, 2025: 03:46:04	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok
153s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:46:04	CMD: cat /tmp/autopkgtest.Uv0c5G/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
153s Wednesday, October 29, 2025: 03:46:04	CMD: cat /tmp/autopkgtest.Uv0c5G/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
153s Wednesday, October 29, 2025: 03:46:04	CMD: touch left.fa.ok
153s Wednesday, October 29, 2025: 03:46:04	CMD: touch right.fa.ok
153s Wednesday, October 29, 2025: 03:46:04	CMD: touch left.fa.ok right.fa.ok
153s Wednesday, October 29, 2025: 03:46:04	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
153s Wednesday, October 29, 2025: 03:46:04	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok
153s -------------------------------------------
153s ----------- Jellyfish  --------------------
153s -- (building a k-mer (25) catalog from reads) --
153s -------------------------------------------
153s 
153s * [Wed Oct 29 03:46:04 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
155s * [Wed Oct 29 03:46:05 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
155s * [Wed Oct 29 03:46:05 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
155s ----------------------------------------------
155s --------------- Inchworm (K=25, asm) ---------------------
155s -- (Linear contig construction from k-mers) --
155s ----------------------------------------------
155s 
155s * [Wed Oct 29 03:46:05 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp
155s Kmer length set to: 25
155s Min assembly length set to: 25
155s Monitor turned on, set to: 1
155s -retaining tmp files
155s min entropy set to: 1
155s setting number of threads to: 1
155s -setting parallel iworm mode.
155s -reading Kmer occurrences...
155s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
155s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
155s 
155s TIMING KMER_DB_BUILDING 0 s.
155s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
155s Pruned 4252 kmers from catalog.
155s 	Pruning time: 0 seconds = 0 minutes.
155s 
155s TIMING PRUNING 0 s.
155s -populating the kmer seed candidate list.
155s Kcounter hash size: 519541
155s Processed 515289 non-zero abundance kmers in kcounter.
155s -Not sorting list of kmers, given parallel mode in effect.
155s -beginning inchworm contig assembly.
155s Total kcounter hash size: 519541 vs. sorted list size: 515289
155s num threads set to: 1
155s Done opening file. tmp.iworm.fa.pid_6646.thread_0
155s 
155s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
155s 
155s TIMING CONTIG_BUILDING 1 s.
155s 
155s TIMING PROG_RUNTIME 1 s.
155s * [Wed Oct 29 03:46:06 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa
155s Wednesday, October 29, 2025: 03:46:06	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished
155s --------------------------------------------------------
155s -------------------- Chrysalis -------------------------
155s -- (Contig Clustering & de Bruijn Graph Construction) --
155s --------------------------------------------------------
155s 
155s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
155s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
155s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
155s * [Wed Oct 29 03:46:06 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100
155s * [Wed Oct 29 03:46:06 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
156s * [Wed Oct 29 03:46:06 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
158s * [Wed Oct 29 03:46:08 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt
158s * [Wed Oct 29 03:46:08 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
159s * [Wed Oct 29 03:46:09 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
159s * [Wed Oct 29 03:46:09 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
159s * [Wed Oct 29 03:46:09 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
159s * [Wed Oct 29 03:46:09 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
159s * [Wed Oct 29 03:46:09 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
160s * [Wed Oct 29 03:46:11 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort
160s Wednesday, October 29, 2025: 03:46:11	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0
160s Wednesday, October 29, 2025: 03:46:11	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok
160s Wednesday, October 29, 2025: 03:46:11	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
160s Wednesday, October 29, 2025: 03:46:11	CMD: touch recursive_trinity.cmds.ok
160s Wednesday, October 29, 2025: 03:46:11	CMD: touch recursive_trinity.cmds.ok
160s 
160s 
160s --------------------------------------------------------------------------------
160s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
160s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
160s --------------------------------------------------------------------------------
160s 
160s Wednesday, October 29, 2025: 03:46:11	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
160s Number of Commands: 36
208s 
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.    
208s 
208s All commands completed successfully. :-)
208s 
208s 
208s 
208s ** Harvesting all assembled transcripts into a single multi-fasta file...
208s 
208s Wednesday, October 29, 2025: 03:46:58	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp
208s * [Wed Oct 29 03:46:58 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1
209s * [Wed Oct 29 03:46:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
209s Wednesday, October 29, 2025: 03:46:59	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map
209s 
209s 
209s #############################################################################
209s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
209s #############################################################################
209s 
209s 
209s 
209s ##### Done Running Trinity #####
209s 
209s if [ $* ]; then
209s     # check full-length reconstruction stats:
209s 
209s     ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90
209s 
209s     ./test_FL.sh --query  trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
209s 
209s fi
209s 
209s ./misc_run_tests/__test_runMe_NO_normalization.sh
209s #!/bin/bash -ve
209s 
209s 
209s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
209s     gunzip -c reads.right.fq.gz > reads.right.fq
209s fi
209s 
209s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
209s     gunzip -c reads.left.fq.gz > reads.left.fq
209s fi
209s 
209s 
209s 
209s #######################################################
209s ##  Run Trinity to Generate Transcriptome Assemblies ##
209s #######################################################
209s 
209s CPU=$(nproc || sysctl -n hw.physicalcpu)
209s 
209s ## use jellyfish
209s ${TRINITY_HOME}/Trinity --seqType fq \
209s               --max_memory 2G \
209s               --left reads.left.fq \
209s               --right reads.right.fq \
209s               --SS_lib_type RF \
209s               --CPU ${CPU} \
209s               --no_normalize_reads \
209s               --output __test_trinity_wo_normalization
209s 
209s 
209s      ______  ____   ____  ____   ____  ______  __ __
209s     |      ||    \ |    ||    \ |    ||      ||  |  |
209s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
209s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
209s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
209s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
209s       |__|  |__|\_||____||__|__||____|  |__|  |____/
209s 
209s     Trinity-v2.15.2
209s 
209s 
209s 
209s Left read files: $VAR1 = [
209s           'reads.left.fq'
209s         ];
209s Right read files: $VAR1 = [
209s           'reads.right.fq'
209s         ];
209s Wednesday, October 29, 2025: 03:46:59	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization
209s Wednesday, October 29, 2025: 03:46:59	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis
209s 
209s 
209s ----------------------------------------------------------------------------------
209s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
209s ----------------------------------------------------------------------------------
209s 
209s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:46:59	CMD: cat /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
209s Wednesday, October 29, 2025: 03:46:59	CMD: cat /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa
209s Wednesday, October 29, 2025: 03:46:59	CMD: touch right.fa.ok
209s Wednesday, October 29, 2025: 03:46:59	CMD: touch left.fa.ok
209s Wednesday, October 29, 2025: 03:46:59	CMD: touch left.fa.ok right.fa.ok
209s Wednesday, October 29, 2025: 03:46:59	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
209s Wednesday, October 29, 2025: 03:46:59	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok
209s -------------------------------------------
209s ----------- Jellyfish  --------------------
209s -- (building a k-mer (25) catalog from reads) --
209s -------------------------------------------
209s 
209s * [Wed Oct 29 03:46:59 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
209s * [Wed Oct 29 03:47:00 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
210s * [Wed Oct 29 03:47:00 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
210s ----------------------------------------------
210s --------------- Inchworm (K=25, asm) ---------------------
210s -- (Linear contig construction from k-mers) --
210s ----------------------------------------------
210s 
210s * [Wed Oct 29 03:47:00 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp
210s Kmer length set to: 25
210s Min assembly length set to: 25
210s Monitor turned on, set to: 1
210s min entropy set to: 1
210s setting number of threads to: 2
210s -setting parallel iworm mode.
210s -reading Kmer occurrences...
210s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
210s  done parsing 520108 Kmers, 520108 added, taking 0 seconds.
210s 
210s TIMING KMER_DB_BUILDING 0 s.
210s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
210s Pruned 4291 kmers from catalog.
210s 	Pruning time: 0 seconds = 0 minutes.
210s 
210s TIMING PRUNING 0 s.
210s -populating the kmer seed candidate list.
210s Kcounter hash size: 520108
210s Processed 515817 non-zero abundance kmers in kcounter.
210s -Not sorting list of kmers, given parallel mode in effect.
210s -beginning inchworm contig assembly.
210s Total kcounter hash size: 520108 vs. sorted list size: 515817
210s num threads set to: 2
210s Done opening file. tmp.iworm.fa.pid_13000.thread_0
210s Done opening file. tmp.iworm.fa.pid_13000.thread_1
210s 
210s 	Iworm contig assembly time: 0 seconds = 0 minutes.
210s 
210s TIMING CONTIG_BUILDING 0 s.
210s 
210s TIMING PROG_RUNTIME 0 s.
210s * [Wed Oct 29 03:47:00 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa
210s Wednesday, October 29, 2025: 03:47:00	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished
210s --------------------------------------------------------
210s -------------------- Chrysalis -------------------------
210s -- (Contig Clustering & de Bruijn Graph Construction) --
210s --------------------------------------------------------
210s 
210s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
210s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
210s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
210s * [Wed Oct 29 03:47:00 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100
210s * [Wed Oct 29 03:47:00 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null
210s * [Wed Oct 29 03:47:00 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 
212s * [Wed Oct 29 03:47:03 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt
213s * [Wed Oct 29 03:47:03 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt
213s * [Wed Oct 29 03:47:04 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted
214s * [Wed Oct 29 03:47:04 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
214s * [Wed Oct 29 03:47:04 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out
214s * [Wed Oct 29 03:47:04 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200
214s * [Wed Oct 29 03:47:04 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
214s * [Wed Oct 29 03:47:05 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort
214s Wednesday, October 29, 2025: 03:47:05	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0
215s Wednesday, October 29, 2025: 03:47:05	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok
215s Wednesday, October 29, 2025: 03:47:05	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
215s Wednesday, October 29, 2025: 03:47:05	CMD: touch recursive_trinity.cmds.ok
215s Wednesday, October 29, 2025: 03:47:05	CMD: touch recursive_trinity.cmds.ok
215s 
215s 
215s --------------------------------------------------------------------------------
215s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
215s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
215s --------------------------------------------------------------------------------
215s 
215s Wednesday, October 29, 2025: 03:47:05	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
215s Number of Commands: 38
248s 
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.    
248s 
248s All commands completed successfully. :-)
248s 
248s 
248s 
248s ** Harvesting all assembled transcripts into a single multi-fasta file...
248s 
248s Wednesday, October 29, 2025: 03:47:39	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp
248s * [Wed Oct 29 03:47:39 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2
249s * [Wed Oct 29 03:47:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
249s Wednesday, October 29, 2025: 03:47:40	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map
249s 
249s 
249s #############################################################################
249s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
249s #############################################################################
249s 
249s 
249s 
249s 
249s 
249s ./misc_run_tests/__runMe_with_qual_trimming.sh
249s #!/bin/bash -ve
249s 
249s 
249s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
249s     gunzip -c reads.right.fq.gz > reads.right.fq
249s fi
249s 
249s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
249s     gunzip -c reads.left.fq.gz > reads.left.fq
249s fi
249s 
249s 
249s 
249s #######################################################
249s ##  Run Trinity to Generate Transcriptome Assemblies ##
249s #######################################################
249s 
249s CPU=$(nproc || sysctl -n hw.physicalcpu)
249s 
249s ${TRINITY_HOME}/Trinity \
249s     --seqType fq \
249s     --max_memory 2G \
249s     --left reads.left.fq \
249s     --right reads.right.fq \
249s     --SS_lib_type RF \
249s     --CPU ${CPU} \
249s     --no_normalize_reads \
249s     --trimmomatic \
249s     --output __test_trinity_with_trimmomatic
250s 
250s 
250s      ______  ____   ____  ____   ____  ______  __ __
250s     |      ||    \ |    ||    \ |    ||      ||  |  |
250s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
250s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
250s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
250s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
250s       |__|  |__|\_||____||__|__||____|  |__|  |____/
250s 
250s     Trinity-v2.15.2
250s 
250s 
250s 
250s Left read files: $VAR1 = [
250s           'reads.left.fq'
250s         ];
250s Right read files: $VAR1 = [
250s           'reads.right.fq'
250s         ];
250s Wednesday, October 29, 2025: 03:47:40	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic
250s Wednesday, October 29, 2025: 03:47:40	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis
250s 
250s 
250s ----------------------------------------------------------------------------------
250s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
250s ----------------------------------------------------------------------------------
250s 
250s ---------------------------------------------------------------
250s ------ Quality Trimming Via Trimmomatic  ---------------------
250s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
250s ---------------------------------------------------------------
250s 
250s 
250s ## Running Trimmomatic on read files: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
250s Wednesday, October 29, 2025: 03:47:40	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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 
250s TrimmomaticPE: Started with arguments:
250s  -threads 2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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
250s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
250s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
250s Quality encoding detected as phred33
250s 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%)
250s TrimmomaticPE: Completed successfully
250s Wednesday, October 29, 2025: 03:47:40	CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq
250s Wednesday, October 29, 2025: 03:47:40	CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq
250s Wednesday, October 29, 2025: 03:47:40	CMD: touch trimmomatic.ok
250s Wednesday, October 29, 2025: 03:47:40	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
250s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:47:40	CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
250s Wednesday, October 29, 2025: 03:47:40	CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa
250s Wednesday, October 29, 2025: 03:47:40	CMD: touch right.fa.ok
250s Wednesday, October 29, 2025: 03:47:40	CMD: touch left.fa.ok
250s Wednesday, October 29, 2025: 03:47:40	CMD: touch left.fa.ok right.fa.ok
250s Wednesday, October 29, 2025: 03:47:40	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
250s Wednesday, October 29, 2025: 03:47:40	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok
250s -------------------------------------------
250s ----------- Jellyfish  --------------------
250s -- (building a k-mer (25) catalog from reads) --
250s -------------------------------------------
250s 
250s * [Wed Oct 29 03:47:40 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
251s * [Wed Oct 29 03:47:41 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
251s * [Wed Oct 29 03:47:41 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
251s ----------------------------------------------
251s --------------- Inchworm (K=25, asm) ---------------------
251s -- (Linear contig construction from k-mers) --
251s ----------------------------------------------
251s 
251s * [Wed Oct 29 03:47:41 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp
251s Kmer length set to: 25
251s Min assembly length set to: 25
251s Monitor turned on, set to: 1
251s min entropy set to: 1
251s setting number of threads to: 2
251s -setting parallel iworm mode.
251s -reading Kmer occurrences...
251s 
 [0M] Kmers parsed.     
251s  done parsing 318541 Kmers, 318541 added, taking 0 seconds.
251s 
251s TIMING KMER_DB_BUILDING 0 s.
251s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
251s Pruned 1498 kmers from catalog.
251s 	Pruning time: 0 seconds = 0 minutes.
251s 
251s TIMING PRUNING 0 s.
251s -populating the kmer seed candidate list.
251s Kcounter hash size: 318541
251s Processed 317043 non-zero abundance kmers in kcounter.
251s -Not sorting list of kmers, given parallel mode in effect.
251s -beginning inchworm contig assembly.
251s Total kcounter hash size: 318541 vs. sorted list size: 317043
251s num threads set to: 2
251s Done opening file. tmp.iworm.fa.pid_19829.thread_0
251s Done opening file. tmp.iworm.fa.pid_19829.thread_1
251s 
251s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
251s 
251s TIMING CONTIG_BUILDING 1 s.
251s 
251s TIMING PROG_RUNTIME 1 s.
251s * [Wed Oct 29 03:47:42 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa
251s Wednesday, October 29, 2025: 03:47:42	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished
251s --------------------------------------------------------
251s -------------------- Chrysalis -------------------------
251s -- (Contig Clustering & de Bruijn Graph Construction) --
251s --------------------------------------------------------
251s 
251s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
251s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
251s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
251s * [Wed Oct 29 03:47:42 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100
251s * [Wed Oct 29 03:47:42 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null
252s * [Wed Oct 29 03:47:42 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 
254s * [Wed Oct 29 03:47:44 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt
254s * [Wed Oct 29 03:47:44 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt
255s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted
255s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
255s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out
255s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200
255s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
256s * [Wed Oct 29 03:47:46 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort
256s Wednesday, October 29, 2025: 03:47:46	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0
256s Wednesday, October 29, 2025: 03:47:47	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok
256s Wednesday, October 29, 2025: 03:47:47	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
256s Wednesday, October 29, 2025: 03:47:47	CMD: touch recursive_trinity.cmds.ok
256s Wednesday, October 29, 2025: 03:47:47	CMD: touch recursive_trinity.cmds.ok
256s 
256s 
256s --------------------------------------------------------------------------------
256s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
256s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
256s --------------------------------------------------------------------------------
256s 
256s Wednesday, October 29, 2025: 03:47:47	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
256s Number of Commands: 35
286s 
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.    
286s 
286s All commands completed successfully. :-)
286s 
286s 
286s 
286s ** Harvesting all assembled transcripts into a single multi-fasta file...
286s 
286s Wednesday, October 29, 2025: 03:48:16	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp
286s * [Wed Oct 29 03:48:16 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2
286s * [Wed Oct 29 03:48:16 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
286s Wednesday, October 29, 2025: 03:48:16	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map
286s 
286s 
286s #############################################################################
286s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
286s #############################################################################
286s 
286s 
286s 
286s ##### Done Running Trinity #####
286s 
286s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
286s #!/bin/bash -ve
286s 
286s 
286s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
286s     gunzip -c reads.right.fq.gz > reads.right.fq
286s fi
286s 
286s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
286s     gunzip -c reads.left.fq.gz > reads.left.fq
286s fi
286s 
286s 
286s 
286s #######################################################
286s ##  Run Trinity to Generate Transcriptome Assemblies ##
286s #######################################################
286s 
286s CPU=$(nproc || sysctl -n hw.physicalcpu)
286s 
286s ${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
286s 
286s 
286s      ______  ____   ____  ____   ____  ______  __ __
286s     |      ||    \ |    ||    \ |    ||      ||  |  |
286s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
286s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
286s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
286s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
286s       |__|  |__|\_||____||__|__||____|  |__|  |____/
286s 
286s     Trinity-v2.15.2
286s 
286s 
286s 
286s Left read files: $VAR1 = [
286s           'reads.left.fq'
286s         ];
286s Right read files: $VAR1 = [
286s           'reads.right.fq'
286s         ];
286s Wednesday, October 29, 2025: 03:48:16	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm
286s Wednesday, October 29, 2025: 03:48:16	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis
286s 
286s 
286s ----------------------------------------------------------------------------------
286s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
286s ----------------------------------------------------------------------------------
286s 
286s ---------------------------------------------------------------
286s ------ Quality Trimming Via Trimmomatic  ---------------------
286s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
286s ---------------------------------------------------------------
286s 
286s 
286s ## Running Trimmomatic on read files: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
286s Wednesday, October 29, 2025: 03:48:16	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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 
286s TrimmomaticPE: Started with arguments:
286s  -threads 2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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
286s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
286s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
286s Quality encoding detected as phred33
287s 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%)
287s TrimmomaticPE: Completed successfully
287s Wednesday, October 29, 2025: 03:48:17	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
287s Wednesday, October 29, 2025: 03:48:17	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
287s Wednesday, October 29, 2025: 03:48:17	CMD: touch trimmomatic.ok
287s Wednesday, October 29, 2025: 03:48:17	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
287s ---------------------------------------------------------------
287s ------------ In silico Read Normalization ---------------------
287s -- (Removing Excess Reads Beyond 200 Coverage --
287s ---------------------------------------------------------------
287s 
287s # running normalization on reads: $VAR1 = [
287s           [
287s             'reads.left.fq.PwU.qtrim.fq'
287s           ],
287s           [
287s             'reads.right.fq.PwU.qtrim.fq'
287s           ]
287s         ];
287s 
287s 
287s Wednesday, October 29, 2025: 03:48:17	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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  
287s -prepping seqs
287s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa
287s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa
287s CMD finished (0 seconds)
287s CMD finished (0 seconds)
287s CMD: touch left.fa.ok
287s CMD finished (0 seconds)
287s CMD: touch right.fa.ok
287s CMD finished (0 seconds)
287s  Done converting input files. CMD: cat left.fa right.fa > both.fa
287s CMD finished (0 seconds)
287s CMD: touch both.fa.ok
287s CMD finished (0 seconds)
287s -kmer counting.
287s -------------------------------------------
287s ----------- Jellyfish  --------------------
287s -- (building a k-mer catalog from reads) --
287s -------------------------------------------
287s 
287s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
288s CMD finished (1 seconds)
288s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
288s CMD finished (0 seconds)
288s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
288s CMD finished (0 seconds)
288s CMD: touch jellyfish.K25.min2.kmers.fa.success
288s CMD finished (0 seconds)
288s -generating stats files
288s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
288s -reading Kmer occurrences...
288s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
288s -reading Kmer occurrences...
288s 
288s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
288s 
288s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
288s STATS_GENERATION_TIME: 0 seconds.
288s CMD finished (0 seconds)
288s STATS_GENERATION_TIME: 0 seconds.
288s CMD finished (0 seconds)
288s CMD: touch left.fa.K25.stats.ok
288s CMD finished (0 seconds)
288s CMD: touch right.fa.K25.stats.ok
288s CMD finished (0 seconds)
288s -sorting each stats file by read name.
288s 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
288s 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
288s CMD finished (0 seconds)
288s CMD finished (0 seconds)
288s CMD: touch left.fa.K25.stats.sort.ok
288s CMD finished (0 seconds)
288s CMD: touch right.fa.K25.stats.sort.ok
288s CMD finished (0 seconds)
288s -defining normalized reads
288s 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
288s -opening left.fa.K25.stats.sort
288s -opening right.fa.K25.stats.sort
288s -done opening files.
288s CMD finished (1 seconds)
288s CMD: touch pairs.K25.stats.ok
288s CMD finished (0 seconds)
288s 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
288s 27678 / 27726 = 99.83% reads selected during normalization.
288s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
288s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
288s CMD finished (0 seconds)
288s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
288s CMD finished (0 seconds)
288s -search and capture.
289s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
289s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq
289s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
289s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq
289s CMD: touch /tmp/autopkgtest.Uv0c5G/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
289s CMD finished (0 seconds)
289s CMD: touch /tmp/autopkgtest.Uv0c5G/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
289s CMD finished (0 seconds)
289s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
289s CMD finished (0 seconds)
289s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
289s CMD finished (0 seconds)
289s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads
289s 
289s 
289s Normalization complete. See outputs: 
289s 	/tmp/autopkgtest.Uv0c5G/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
289s 	/tmp/autopkgtest.Uv0c5G/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
289s Wednesday, October 29, 2025: 03:48:19	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok
289s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:48:19	CMD: cat /tmp/autopkgtest.Uv0c5G/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
289s Wednesday, October 29, 2025: 03:48:19	CMD: cat /tmp/autopkgtest.Uv0c5G/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
289s Wednesday, October 29, 2025: 03:48:19	CMD: touch left.fa.ok
289s Wednesday, October 29, 2025: 03:48:19	CMD: touch right.fa.ok
289s Wednesday, October 29, 2025: 03:48:19	CMD: touch left.fa.ok right.fa.ok
289s Wednesday, October 29, 2025: 03:48:19	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
289s Wednesday, October 29, 2025: 03:48:19	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok
289s -------------------------------------------
289s ----------- Jellyfish  --------------------
289s -- (building a k-mer (25) catalog from reads) --
289s -------------------------------------------
289s 
289s * [Wed Oct 29 03:48:19 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
289s * [Wed Oct 29 03:48:20 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
289s * [Wed Oct 29 03:48:20 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
290s ----------------------------------------------
290s --------------- Inchworm (K=25, asm) ---------------------
290s -- (Linear contig construction from k-mers) --
290s ----------------------------------------------
290s 
290s * [Wed Oct 29 03:48:20 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp
290s Kmer length set to: 25
290s Min assembly length set to: 25
290s Monitor turned on, set to: 1
290s min entropy set to: 1
290s setting number of threads to: 2
290s -setting parallel iworm mode.
290s -reading Kmer occurrences...
290s 
 [0M] Kmers parsed.     
290s  done parsing 311705 Kmers, 311705 added, taking 0 seconds.
290s 
290s TIMING KMER_DB_BUILDING 0 s.
290s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
290s Pruned 1486 kmers from catalog.
290s 	Pruning time: 0 seconds = 0 minutes.
290s 
290s TIMING PRUNING 0 s.
290s -populating the kmer seed candidate list.
290s Kcounter hash size: 311705
290s Processed 310219 non-zero abundance kmers in kcounter.
290s -Not sorting list of kmers, given parallel mode in effect.
290s -beginning inchworm contig assembly.
290s Total kcounter hash size: 311705 vs. sorted list size: 310219
290s num threads set to: 2
290s Done opening file. tmp.iworm.fa.pid_26210.thread_0
290s Done opening file. tmp.iworm.fa.pid_26210.thread_1
290s 
290s 	Iworm contig assembly time: 0 seconds = 0 minutes.
290s 
290s TIMING CONTIG_BUILDING 0 s.
290s 
290s TIMING PROG_RUNTIME 0 s.
290s * [Wed Oct 29 03:48:20 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa
290s Wednesday, October 29, 2025: 03:48:20	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished
290s --------------------------------------------------------
290s -------------------- Chrysalis -------------------------
290s -- (Contig Clustering & de Bruijn Graph Construction) --
290s --------------------------------------------------------
290s 
290s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
290s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
290s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
290s * [Wed Oct 29 03:48:20 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100
290s * [Wed Oct 29 03:48:20 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null
290s * [Wed Oct 29 03:48:20 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 
292s * [Wed Oct 29 03:48:22 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt
292s * [Wed Oct 29 03:48:22 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/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 
294s * [Wed Oct 29 03:48:24 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort
294s Wednesday, October 29, 2025: 03:48:24	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0
294s Wednesday, October 29, 2025: 03:48:25	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok
294s Wednesday, October 29, 2025: 03:48:25	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
294s Wednesday, October 29, 2025: 03:48:25	CMD: touch recursive_trinity.cmds.ok
294s Wednesday, October 29, 2025: 03:48:25	CMD: touch recursive_trinity.cmds.ok
294s 
294s 
294s --------------------------------------------------------------------------------
294s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
294s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
294s --------------------------------------------------------------------------------
294s 
294s Wednesday, October 29, 2025: 03:48:25	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
294s Number of Commands: 39
324s 
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.    
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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.    
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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.    
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succeeded(32)   82.0513% completed.    
succeeded(33)   84.6154% completed.    
succeeded(34)   87.1795% completed.    
succeeded(35)   89.7436% completed.    
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succeeded(37)   94.8718% completed.    
succeeded(38)   97.4359% completed.    
succeeded(39)   100% completed.    
324s 
324s All commands completed successfully. :-)
324s 
324s 
324s 
324s ** Harvesting all assembled transcripts into a single multi-fasta file...
324s 
324s Wednesday, October 29, 2025: 03:48:54	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp
324s * [Wed Oct 29 03:48:54 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2
324s * [Wed Oct 29 03:48:54 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
324s Wednesday, October 29, 2025: 03:48:54	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map
324s 
324s 
324s #############################################################################
324s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
324s #############################################################################
324s 
324s 
324s 
324s ##### Done Running Trinity #####
324s 
324s exit 0
324s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh
324s #!/bin/bash -ve
324s 
324s ${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
324s 
324s 
324s      ______  ____   ____  ____   ____  ______  __ __
324s     |      ||    \ |    ||    \ |    ||      ||  |  |
324s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
324s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
324s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
324s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
324s       |__|  |__|\_||____||__|__||____|  |__|  |____/
324s 
324s     Trinity-v2.15.2
324s 
324s 
324s 
324s Left read files: $VAR1 = [
324s           'reads.left.fq.gz'
324s         ];
324s Right read files: $VAR1 = [
324s           'reads.right.fq.gz'
324s         ];
324s Wednesday, October 29, 2025: 03:48:54	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard
324s Wednesday, October 29, 2025: 03:48:54	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis
324s 
324s 
324s ----------------------------------------------------------------------------------
324s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
324s ----------------------------------------------------------------------------------
324s 
324s ---------------------------------------------------------------
324s ------------ In silico Read Normalization ---------------------
324s -- (Removing Excess Reads Beyond 200 Coverage --
324s ---------------------------------------------------------------
324s 
324s # running normalization on reads: $VAR1 = [
324s           [
324s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
324s           ],
324s           [
324s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
324s           ]
324s         ];
324s 
324s 
324s Wednesday, October 29, 2025: 03:48:54	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
324s -prepping seqs
324s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
324s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
324s CMD finished (0 seconds)
324s CMD finished (0 seconds)
324s CMD: touch left.fa.ok
324s CMD finished (0 seconds)
324s CMD: touch right.fa.ok
324s CMD finished (0 seconds)
324s  Done converting input files. CMD: cat left.fa right.fa > both.fa
324s CMD finished (0 seconds)
324s CMD: touch both.fa.ok
324s CMD finished (0 seconds)
324s -kmer counting.
324s -------------------------------------------
324s ----------- Jellyfish  --------------------
324s -- (building a k-mer catalog from reads) --
324s -------------------------------------------
324s 
324s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
325s CMD finished (2 seconds)
325s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
325s CMD finished (0 seconds)
325s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
325s CMD finished (0 seconds)
325s CMD: touch jellyfish.K25.min2.kmers.fa.success
325s CMD finished (0 seconds)
325s -generating stats files
325s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
325s -reading Kmer occurrences...
325s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
325s -reading Kmer occurrences...
325s 
325s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
325s 
325s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
326s STATS_GENERATION_TIME: 0 seconds.
326s CMD finished (0 seconds)
326s STATS_GENERATION_TIME: 0 seconds.
326s CMD finished (0 seconds)
326s CMD: touch left.fa.K25.stats.ok
326s CMD finished (0 seconds)
326s CMD: touch right.fa.K25.stats.ok
326s CMD finished (0 seconds)
326s -sorting each stats file by read name.
326s 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
326s 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
326s CMD finished (0 seconds)
326s CMD finished (0 seconds)
326s CMD: touch left.fa.K25.stats.sort.ok
326s CMD finished (0 seconds)
326s CMD: touch right.fa.K25.stats.sort.ok
326s CMD finished (0 seconds)
326s -defining normalized reads
326s 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
326s -opening left.fa.K25.stats.sort
326s -opening right.fa.K25.stats.sort
326s -done opening files.
326s CMD finished (0 seconds)
326s CMD: touch pairs.K25.stats.ok
326s CMD finished (0 seconds)
326s 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
326s 30472 / 30575 = 99.66% reads selected during normalization.
326s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
326s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
326s CMD finished (0 seconds)
326s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
326s CMD finished (0 seconds)
326s -search and capture.
326s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
326s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
326s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
326s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
326s CMD: touch /tmp/autopkgtest.Uv0c5G/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
326s CMD finished (0 seconds)
326s CMD: touch /tmp/autopkgtest.Uv0c5G/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
326s CMD finished (0 seconds)
326s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
326s CMD finished (0 seconds)
326s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
326s CMD finished (0 seconds)
326s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads
326s 
326s 
326s Normalization complete. See outputs: 
326s 	/tmp/autopkgtest.Uv0c5G/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
326s 	/tmp/autopkgtest.Uv0c5G/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
326s Wednesday, October 29, 2025: 03:48:57	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok
326s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:48:57	CMD: cat /tmp/autopkgtest.Uv0c5G/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
326s Wednesday, October 29, 2025: 03:48:57	CMD: cat /tmp/autopkgtest.Uv0c5G/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
326s Wednesday, October 29, 2025: 03:48:57	CMD: touch left.fa.ok
326s Wednesday, October 29, 2025: 03:48:57	CMD: touch right.fa.ok
326s Wednesday, October 29, 2025: 03:48:57	CMD: touch left.fa.ok right.fa.ok
326s Wednesday, October 29, 2025: 03:48:57	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
326s Wednesday, October 29, 2025: 03:48:57	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok
326s -------------------------------------------
326s ----------- Jellyfish  --------------------
326s -- (building a k-mer (25) catalog from reads) --
326s -------------------------------------------
326s 
326s * [Wed Oct 29 03:48:57 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
328s * [Wed Oct 29 03:48:58 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
328s * [Wed Oct 29 03:48:58 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
328s ----------------------------------------------
328s --------------- Inchworm (K=25, asm) ---------------------
328s -- (Linear contig construction from k-mers) --
328s ----------------------------------------------
328s 
328s * [Wed Oct 29 03:48:58 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp
328s Kmer length set to: 25
328s Min assembly length set to: 25
328s Monitor turned on, set to: 1
328s min entropy set to: 1
328s setting number of threads to: 1
328s -setting parallel iworm mode.
328s -reading Kmer occurrences...
328s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
328s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
328s 
328s TIMING KMER_DB_BUILDING 0 s.
328s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
328s Pruned 4252 kmers from catalog.
328s 	Pruning time: 0 seconds = 0 minutes.
328s 
328s TIMING PRUNING 0 s.
328s -populating the kmer seed candidate list.
328s Kcounter hash size: 519541
328s Processed 515289 non-zero abundance kmers in kcounter.
328s -Not sorting list of kmers, given parallel mode in effect.
328s -beginning inchworm contig assembly.
328s Total kcounter hash size: 519541 vs. sorted list size: 515289
328s num threads set to: 1
328s Done opening file. tmp.iworm.fa.pid_33232.thread_0
328s 
328s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
328s 
328s TIMING CONTIG_BUILDING 1 s.
328s 
328s TIMING PROG_RUNTIME 1 s.
328s * [Wed Oct 29 03:48:59 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa
328s Wednesday, October 29, 2025: 03:48:59	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished
328s --------------------------------------------------------
328s -------------------- Chrysalis -------------------------
328s -- (Contig Clustering & de Bruijn Graph Construction) --
328s --------------------------------------------------------
328s 
328s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
328s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
328s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
329s * [Wed Oct 29 03:48:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100
329s * [Wed Oct 29 03:48:59 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null
329s * [Wed Oct 29 03:48:59 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 
331s * [Wed Oct 29 03:49:01 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt
331s * [Wed Oct 29 03:49:01 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt
332s * [Wed Oct 29 03:49:02 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted
332s * [Wed Oct 29 03:49:02 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
332s * [Wed Oct 29 03:49:02 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out
332s * [Wed Oct 29 03:49:02 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200
332s * [Wed Oct 29 03:49:02 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
333s * [Wed Oct 29 03:49:04 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort
333s Wednesday, October 29, 2025: 03:49:04	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0
334s Wednesday, October 29, 2025: 03:49:04	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok
334s Wednesday, October 29, 2025: 03:49:04	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
334s Wednesday, October 29, 2025: 03:49:04	CMD: touch recursive_trinity.cmds.ok
334s Wednesday, October 29, 2025: 03:49:04	CMD: touch recursive_trinity.cmds.ok
334s 
334s 
334s --------------------------------------------------------------------------------
334s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
334s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
334s --------------------------------------------------------------------------------
334s 
334s Wednesday, October 29, 2025: 03:49:04	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
334s Number of Commands: 36
334s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
334s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
334s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
334s bt2 index files: $VAR1 = [];
334s Note - bowtie-build indices do not yet exist. Indexing genome now.
334s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
334s CMD: touch /tmp/autopkgtest.Uv0c5G/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
334s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
335s 9900 reads; of these:
335s   9900 (100.00%) were unpaired; of these:
335s     5 (0.05%) aligned 0 times
335s     5821 (58.80%) aligned exactly 1 time
335s     4074 (41.15%) aligned >1 times
335s 99.95% overall alignment rate
335s CMD: touch /tmp/autopkgtest.Uv0c5G/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
335s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
335s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
335s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
335s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
335s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
335s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
335s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
335s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
335s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
335s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
335s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
335s 
335s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
335s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
335s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
335s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
335s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
335s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
335s -processing jaccard pair sensor
335s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
336s 
[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
336s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
339s 
succeeded(1)   2.77778% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
339s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
339s bt2 index files: $VAR1 = [];
339s Note - bowtie-build indices do not yet exist. Indexing genome now.
339s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
339s CMD: touch /tmp/autopkgtest.Uv0c5G/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
339s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
339s 6 reads; of these:
339s   6 (100.00%) were unpaired; of these:
339s     0 (0.00%) aligned 0 times
339s     6 (100.00%) aligned exactly 1 time
339s     0 (0.00%) aligned >1 times
339s 100.00% overall alignment rate
339s CMD: touch /tmp/autopkgtest.Uv0c5G/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
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
339s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
339s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
339s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
339s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
339s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
339s 
339s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
339s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
339s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
339s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
339s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
339s -processing jaccard pair sensor
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
339s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
340s 
succeeded(2)   5.55556% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
340s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
340s bt2 index files: $VAR1 = [];
340s Note - bowtie-build indices do not yet exist. Indexing genome now.
340s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
340s CMD: touch /tmp/autopkgtest.Uv0c5G/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
340s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
340s 29 reads; of these:
340s   29 (100.00%) were unpaired; of these:
340s     0 (0.00%) aligned 0 times
340s     29 (100.00%) aligned exactly 1 time
340s     0 (0.00%) aligned >1 times
340s 100.00% overall alignment rate
340s CMD: touch /tmp/autopkgtest.Uv0c5G/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
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
340s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
340s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
340s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
340s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
340s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
340s 
340s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
340s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
340s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
340s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
340s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
340s -processing jaccard pair sensor
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
340s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
341s 
succeeded(3)   8.33333% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
341s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
341s bt2 index files: $VAR1 = [];
341s Note - bowtie-build indices do not yet exist. Indexing genome now.
341s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
341s CMD: touch /tmp/autopkgtest.Uv0c5G/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
341s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
341s 33 reads; of these:
341s   33 (100.00%) were unpaired; of these:
341s     0 (0.00%) aligned 0 times
341s     33 (100.00%) aligned exactly 1 time
341s     0 (0.00%) aligned >1 times
341s 100.00% overall alignment rate
341s CMD: touch /tmp/autopkgtest.Uv0c5G/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
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
341s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
341s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
341s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
341s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
341s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
341s 
341s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
341s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
341s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
341s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
341s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
341s -processing jaccard pair sensor
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
341s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
342s 
succeeded(4)   11.1111% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
342s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
342s bt2 index files: $VAR1 = [];
342s Note - bowtie-build indices do not yet exist. Indexing genome now.
342s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
342s CMD: touch /tmp/autopkgtest.Uv0c5G/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
342s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
342s 9 reads; of these:
342s   9 (100.00%) were unpaired; of these:
342s     0 (0.00%) aligned 0 times
342s     9 (100.00%) aligned exactly 1 time
342s     0 (0.00%) aligned >1 times
342s 100.00% overall alignment rate
342s CMD: touch /tmp/autopkgtest.Uv0c5G/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
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
342s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
342s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
342s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
342s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
342s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
342s 
342s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
342s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
342s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
342s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
342s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
342s -processing jaccard pair sensor
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
342s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
343s 
succeeded(5)   13.8889% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
343s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
343s bt2 index files: $VAR1 = [];
343s Note - bowtie-build indices do not yet exist. Indexing genome now.
343s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
343s CMD: touch /tmp/autopkgtest.Uv0c5G/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
343s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
343s 8 reads; of these:
343s   8 (100.00%) were unpaired; of these:
343s     0 (0.00%) aligned 0 times
343s     8 (100.00%) aligned exactly 1 time
343s     0 (0.00%) aligned >1 times
343s 100.00% overall alignment rate
343s CMD: touch /tmp/autopkgtest.Uv0c5G/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
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
343s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
343s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
343s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
343s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
343s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
343s 
343s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
343s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
343s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
343s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
343s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
343s -processing jaccard pair sensor
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
343s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
344s 
succeeded(6)   16.6667% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
344s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
344s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
344s bt2 index files: $VAR1 = [];
344s Note - bowtie-build indices do not yet exist. Indexing genome now.
344s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
344s CMD: touch /tmp/autopkgtest.Uv0c5G/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
344s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
345s 4987 reads; of these:
345s   4987 (100.00%) were unpaired; of these:
345s     2 (0.04%) aligned 0 times
345s     2643 (53.00%) aligned exactly 1 time
345s     2342 (46.96%) aligned >1 times
345s 99.96% overall alignment rate
345s CMD: touch /tmp/autopkgtest.Uv0c5G/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
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
345s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
345s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
345s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
345s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
345s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
345s 
345s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
345s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
345s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
345s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
345s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
345s -processing jaccard pair sensor
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
345s 
[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
345s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
347s 
succeeded(7)   19.4444% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
347s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
347s bt2 index files: $VAR1 = [];
347s Note - bowtie-build indices do not yet exist. Indexing genome now.
347s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
347s CMD: touch /tmp/autopkgtest.Uv0c5G/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
347s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
347s 15 reads; of these:
347s   15 (100.00%) were unpaired; of these:
347s     0 (0.00%) aligned 0 times
347s     15 (100.00%) aligned exactly 1 time
347s     0 (0.00%) aligned >1 times
347s 100.00% overall alignment rate
347s CMD: touch /tmp/autopkgtest.Uv0c5G/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
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
347s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
347s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
347s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
347s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
347s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
347s 
347s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
347s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
347s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
347s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
347s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
347s -processing jaccard pair sensor
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
347s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
348s 
succeeded(8)   22.2222% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
348s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
348s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
348s bt2 index files: $VAR1 = [];
348s Note - bowtie-build indices do not yet exist. Indexing genome now.
348s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
348s CMD: touch /tmp/autopkgtest.Uv0c5G/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
348s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
348s 17 reads; of these:
348s   17 (100.00%) were unpaired; of these:
348s     0 (0.00%) aligned 0 times
348s     17 (100.00%) aligned exactly 1 time
348s     0 (0.00%) aligned >1 times
348s 100.00% overall alignment rate
348s CMD: touch /tmp/autopkgtest.Uv0c5G/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
348s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
348s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
348s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
348s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
348s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
348s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
348s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
349s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
349s 
349s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
349s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
349s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
349s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
349s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
349s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
349s -processing jaccard pair sensor
349s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
349s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
349s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
350s 
succeeded(9)   25% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
350s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
350s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
350s bt2 index files: $VAR1 = [];
350s Note - bowtie-build indices do not yet exist. Indexing genome now.
350s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
350s CMD: touch /tmp/autopkgtest.Uv0c5G/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
350s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
350s 7052 reads; of these:
350s   7052 (100.00%) were unpaired; of these:
350s     4 (0.06%) aligned 0 times
350s     5120 (72.60%) aligned exactly 1 time
350s     1928 (27.34%) aligned >1 times
350s 99.94% overall alignment rate
350s CMD: touch /tmp/autopkgtest.Uv0c5G/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
350s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
350s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
350s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
350s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
350s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
350s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
350s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
350s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
350s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
350s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
350s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
350s 
350s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
350s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
350s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
350s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
350s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
350s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
350s -processing jaccard pair sensor
351s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
351s 
[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
351s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
357s 
succeeded(10)   27.7778% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
357s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
357s bt2 index files: $VAR1 = [];
357s Note - bowtie-build indices do not yet exist. Indexing genome now.
357s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
357s CMD: touch /tmp/autopkgtest.Uv0c5G/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
357s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
357s 7 reads; of these:
357s   7 (100.00%) were unpaired; of these:
357s     3 (42.86%) aligned 0 times
357s     4 (57.14%) aligned exactly 1 time
357s     0 (0.00%) aligned >1 times
357s 57.14% overall alignment rate
357s CMD: touch /tmp/autopkgtest.Uv0c5G/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
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
357s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
357s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
357s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
357s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
357s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
357s 
357s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
357s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
357s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
357s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
357s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
357s -processing jaccard pair sensor
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
357s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
358s 
succeeded(11)   30.5556% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
358s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
358s bt2 index files: $VAR1 = [];
358s Note - bowtie-build indices do not yet exist. Indexing genome now.
358s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
358s CMD: touch /tmp/autopkgtest.Uv0c5G/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
358s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
358s 28 reads; of these:
358s   28 (100.00%) were unpaired; of these:
358s     0 (0.00%) aligned 0 times
358s     28 (100.00%) aligned exactly 1 time
358s     0 (0.00%) aligned >1 times
358s 100.00% overall alignment rate
358s CMD: touch /tmp/autopkgtest.Uv0c5G/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
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
358s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
358s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
358s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
358s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
358s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
358s 
358s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
358s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
358s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
358s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
358s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
358s -processing jaccard pair sensor
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
358s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
359s 
succeeded(12)   33.3333% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
359s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
359s bt2 index files: $VAR1 = [];
359s Note - bowtie-build indices do not yet exist. Indexing genome now.
359s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
359s CMD: touch /tmp/autopkgtest.Uv0c5G/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
359s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
359s 24 reads; of these:
359s   24 (100.00%) were unpaired; of these:
359s     0 (0.00%) aligned 0 times
359s     24 (100.00%) aligned exactly 1 time
359s     0 (0.00%) aligned >1 times
359s 100.00% overall alignment rate
359s CMD: touch /tmp/autopkgtest.Uv0c5G/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
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
359s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
359s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
359s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
359s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
359s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
359s 
359s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
359s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
359s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
359s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
359s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
359s -processing jaccard pair sensor
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
359s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
360s 
succeeded(13)   36.1111% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
360s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
360s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
360s bt2 index files: $VAR1 = [];
360s Note - bowtie-build indices do not yet exist. Indexing genome now.
360s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
360s CMD: touch /tmp/autopkgtest.Uv0c5G/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
360s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
361s 5130 reads; of these:
361s   5130 (100.00%) were unpaired; of these:
361s     6 (0.12%) aligned 0 times
361s     4306 (83.94%) aligned exactly 1 time
361s     818 (15.95%) aligned >1 times
361s 99.88% overall alignment rate
361s CMD: touch /tmp/autopkgtest.Uv0c5G/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
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
361s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
361s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
361s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
361s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
361s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
361s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
361s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
361s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
361s 
361s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
361s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
361s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
361s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
361s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
361s -processing jaccard pair sensor
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
361s 
[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
361s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
364s 
succeeded(14)   38.8889% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
364s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
364s bt2 index files: $VAR1 = [];
364s Note - bowtie-build indices do not yet exist. Indexing genome now.
364s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
364s CMD: touch /tmp/autopkgtest.Uv0c5G/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
364s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
364s 3374 reads; of these:
364s   3374 (100.00%) were unpaired; of these:
364s     1 (0.03%) aligned 0 times
364s     2870 (85.06%) aligned exactly 1 time
364s     503 (14.91%) aligned >1 times
364s 99.97% overall alignment rate
364s CMD: touch /tmp/autopkgtest.Uv0c5G/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
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
364s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
364s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
364s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
364s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
364s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
364s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
364s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
364s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
364s 
364s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
364s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
364s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
364s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
364s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
364s -processing jaccard pair sensor
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
364s 
[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
364s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
366s 
succeeded(15)   41.6667% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
366s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
366s bt2 index files: $VAR1 = [];
366s Note - bowtie-build indices do not yet exist. Indexing genome now.
366s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
366s CMD: touch /tmp/autopkgtest.Uv0c5G/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
366s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
366s 6 reads; of these:
366s   6 (100.00%) were unpaired; of these:
366s     0 (0.00%) aligned 0 times
366s     6 (100.00%) aligned exactly 1 time
366s     0 (0.00%) aligned >1 times
366s 100.00% overall alignment rate
366s CMD: touch /tmp/autopkgtest.Uv0c5G/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
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
366s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
366s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
366s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
366s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
366s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
366s 
366s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
366s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
366s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
366s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
366s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
366s -processing jaccard pair sensor
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
366s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
367s 
succeeded(16)   44.4444% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
367s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
367s bt2 index files: $VAR1 = [];
367s Note - bowtie-build indices do not yet exist. Indexing genome now.
367s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
367s CMD: touch /tmp/autopkgtest.Uv0c5G/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
367s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
367s 8 reads; of these:
367s   8 (100.00%) were unpaired; of these:
367s     0 (0.00%) aligned 0 times
367s     8 (100.00%) aligned exactly 1 time
367s     0 (0.00%) aligned >1 times
367s 100.00% overall alignment rate
367s CMD: touch /tmp/autopkgtest.Uv0c5G/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
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
367s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
367s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
367s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
367s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
367s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
367s 
367s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
367s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
367s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
367s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
367s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
367s -processing jaccard pair sensor
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
367s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
368s 
succeeded(17)   47.2222% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
368s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
368s bt2 index files: $VAR1 = [];
368s Note - bowtie-build indices do not yet exist. Indexing genome now.
368s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
368s CMD: touch /tmp/autopkgtest.Uv0c5G/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
368s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
368s 14 reads; of these:
368s   14 (100.00%) were unpaired; of these:
368s     0 (0.00%) aligned 0 times
368s     14 (100.00%) aligned exactly 1 time
368s     0 (0.00%) aligned >1 times
368s 100.00% overall alignment rate
368s CMD: touch /tmp/autopkgtest.Uv0c5G/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
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
368s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
368s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
368s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
368s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
368s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
368s 
368s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
368s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
368s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
368s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
368s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
368s -processing jaccard pair sensor
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
368s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
369s 
succeeded(18)   50% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
369s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
369s bt2 index files: $VAR1 = [];
369s Note - bowtie-build indices do not yet exist. Indexing genome now.
369s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
369s CMD: touch /tmp/autopkgtest.Uv0c5G/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
369s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
369s 15 reads; of these:
369s   15 (100.00%) were unpaired; of these:
369s     0 (0.00%) aligned 0 times
369s     15 (100.00%) aligned exactly 1 time
369s     0 (0.00%) aligned >1 times
369s 100.00% overall alignment rate
369s CMD: touch /tmp/autopkgtest.Uv0c5G/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
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
369s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
369s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
369s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
369s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
369s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
369s 
369s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
369s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
369s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
369s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
369s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
369s -processing jaccard pair sensor
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
369s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
370s 
succeeded(19)   52.7778% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
370s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
370s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
370s bt2 index files: $VAR1 = [];
370s Note - bowtie-build indices do not yet exist. Indexing genome now.
370s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
371s CMD: touch /tmp/autopkgtest.Uv0c5G/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
371s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
371s 2351 reads; of these:
371s   2351 (100.00%) were unpaired; of these:
371s     1 (0.04%) aligned 0 times
371s     1736 (73.84%) aligned exactly 1 time
371s     614 (26.12%) aligned >1 times
371s 99.96% overall alignment rate
371s CMD: touch /tmp/autopkgtest.Uv0c5G/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
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
371s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
371s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
371s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
371s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
371s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
371s 
371s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
371s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
371s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
371s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
371s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
371s -processing jaccard pair sensor
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
371s 
[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
371s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
373s 
succeeded(20)   55.5556% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
373s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
373s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
373s bt2 index files: $VAR1 = [];
373s Note - bowtie-build indices do not yet exist. Indexing genome now.
373s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
373s CMD: touch /tmp/autopkgtest.Uv0c5G/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
373s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
373s 1875 reads; of these:
373s   1875 (100.00%) were unpaired; of these:
373s     2 (0.11%) aligned 0 times
373s     1543 (82.29%) aligned exactly 1 time
373s     330 (17.60%) aligned >1 times
373s 99.89% overall alignment rate
373s CMD: touch /tmp/autopkgtest.Uv0c5G/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
373s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
373s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
373s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
373s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
373s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
373s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
373s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
373s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
373s 
374s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
374s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
374s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
374s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
374s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
374s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
374s -processing jaccard pair sensor
374s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
374s 
[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
374s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
375s 
succeeded(21)   58.3333% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
375s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
375s bt2 index files: $VAR1 = [];
375s Note - bowtie-build indices do not yet exist. Indexing genome now.
375s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
375s CMD: touch /tmp/autopkgtest.Uv0c5G/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
375s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
375s 40 reads; of these:
375s   40 (100.00%) were unpaired; of these:
375s     0 (0.00%) aligned 0 times
375s     36 (90.00%) aligned exactly 1 time
375s     4 (10.00%) aligned >1 times
375s 100.00% overall alignment rate
375s CMD: touch /tmp/autopkgtest.Uv0c5G/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
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
375s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
375s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
375s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
375s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
375s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
375s 
375s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
375s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
375s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
375s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
375s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
375s -processing jaccard pair sensor
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
375s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
376s 
succeeded(22)   61.1111% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
376s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
376s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
376s bt2 index files: $VAR1 = [];
376s Note - bowtie-build indices do not yet exist. Indexing genome now.
376s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
376s CMD: touch /tmp/autopkgtest.Uv0c5G/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
376s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
376s 28 reads; of these:
376s   28 (100.00%) were unpaired; of these:
376s     0 (0.00%) aligned 0 times
376s     28 (100.00%) aligned exactly 1 time
376s     0 (0.00%) aligned >1 times
376s 100.00% overall alignment rate
376s CMD: touch /tmp/autopkgtest.Uv0c5G/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
376s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
377s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
377s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
377s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
377s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
377s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
377s 
377s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
377s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
377s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
377s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
377s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
377s -processing jaccard pair sensor
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
377s 
succeeded(23)   63.8889% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
377s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
377s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
377s bt2 index files: $VAR1 = [];
377s Note - bowtie-build indices do not yet exist. Indexing genome now.
377s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
378s CMD: touch /tmp/autopkgtest.Uv0c5G/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
378s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
378s 29 reads; of these:
378s   29 (100.00%) were unpaired; of these:
378s     0 (0.00%) aligned 0 times
378s     23 (79.31%) aligned exactly 1 time
378s     6 (20.69%) aligned >1 times
378s 100.00% overall alignment rate
378s CMD: touch /tmp/autopkgtest.Uv0c5G/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
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
378s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
378s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
378s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
378s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
378s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
378s 
378s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
378s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
378s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
378s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
378s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
378s -processing jaccard pair sensor
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
378s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
379s 
succeeded(24)   66.6667% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
379s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
379s bt2 index files: $VAR1 = [];
379s Note - bowtie-build indices do not yet exist. Indexing genome now.
379s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
379s CMD: touch /tmp/autopkgtest.Uv0c5G/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
379s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
379s 8 reads; of these:
379s   8 (100.00%) were unpaired; of these:
379s     0 (0.00%) aligned 0 times
379s     8 (100.00%) aligned exactly 1 time
379s     0 (0.00%) aligned >1 times
379s 100.00% overall alignment rate
379s CMD: touch /tmp/autopkgtest.Uv0c5G/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
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
379s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
379s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
379s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
379s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
379s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
379s 
379s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
379s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
379s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
379s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
379s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
379s -processing jaccard pair sensor
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
379s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
380s 
succeeded(25)   69.4444% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
380s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
380s bt2 index files: $VAR1 = [];
380s Note - bowtie-build indices do not yet exist. Indexing genome now.
380s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
380s CMD: touch /tmp/autopkgtest.Uv0c5G/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
380s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
380s 81 reads; of these:
380s   81 (100.00%) were unpaired; of these:
380s     0 (0.00%) aligned 0 times
380s     78 (96.30%) aligned exactly 1 time
380s     3 (3.70%) aligned >1 times
380s 100.00% overall alignment rate
380s CMD: touch /tmp/autopkgtest.Uv0c5G/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
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
380s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
380s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
380s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
380s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
380s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
380s 
380s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
380s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
380s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
380s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
380s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
380s -processing jaccard pair sensor
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
380s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
381s 
succeeded(26)   72.2222% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
381s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
381s bt2 index files: $VAR1 = [];
381s Note - bowtie-build indices do not yet exist. Indexing genome now.
381s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
381s CMD: touch /tmp/autopkgtest.Uv0c5G/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
381s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
381s 13 reads; of these:
381s   13 (100.00%) were unpaired; of these:
381s     0 (0.00%) aligned 0 times
381s     13 (100.00%) aligned exactly 1 time
381s     0 (0.00%) aligned >1 times
381s 100.00% overall alignment rate
381s CMD: touch /tmp/autopkgtest.Uv0c5G/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
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
381s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
381s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
381s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
381s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
381s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
381s 
381s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
381s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
381s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
381s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
381s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
381s -processing jaccard pair sensor
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
381s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
382s 
succeeded(27)   75% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
382s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
382s bt2 index files: $VAR1 = [];
382s Note - bowtie-build indices do not yet exist. Indexing genome now.
382s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
382s CMD: touch /tmp/autopkgtest.Uv0c5G/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
382s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
382s 1556 reads; of these:
382s   1556 (100.00%) were unpaired; of these:
382s     1 (0.06%) aligned 0 times
382s     1328 (85.35%) aligned exactly 1 time
382s     227 (14.59%) aligned >1 times
382s 99.94% overall alignment rate
382s CMD: touch /tmp/autopkgtest.Uv0c5G/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
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
382s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
382s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
382s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
382s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
382s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
382s 
382s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
382s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
382s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
382s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
382s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
382s -processing jaccard pair sensor
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
382s 
[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
382s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
384s 
succeeded(28)   77.7778% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
384s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
384s bt2 index files: $VAR1 = [];
384s Note - bowtie-build indices do not yet exist. Indexing genome now.
384s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
384s CMD: touch /tmp/autopkgtest.Uv0c5G/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
384s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
384s 20 reads; of these:
384s   20 (100.00%) were unpaired; of these:
384s     0 (0.00%) aligned 0 times
384s     20 (100.00%) aligned exactly 1 time
384s     0 (0.00%) aligned >1 times
384s 100.00% overall alignment rate
384s CMD: touch /tmp/autopkgtest.Uv0c5G/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
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
384s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
384s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
384s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
384s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
384s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
384s 
384s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
384s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
384s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
384s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
384s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
384s -processing jaccard pair sensor
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
384s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
385s 
succeeded(29)   80.5556% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
385s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
385s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
385s bt2 index files: $VAR1 = [];
385s Note - bowtie-build indices do not yet exist. Indexing genome now.
385s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
385s CMD: touch /tmp/autopkgtest.Uv0c5G/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
385s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
386s 8656 reads; of these:
386s   8656 (100.00%) were unpaired; of these:
386s     6 (0.07%) aligned 0 times
386s     5677 (65.58%) aligned exactly 1 time
386s     2973 (34.35%) aligned >1 times
386s 99.93% overall alignment rate
386s CMD: touch /tmp/autopkgtest.Uv0c5G/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
386s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
386s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
386s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
386s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
386s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
386s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
386s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
386s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
386s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
386s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
386s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
386s 
386s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
386s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
386s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
386s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
386s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
386s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
386s -processing jaccard pair sensor
386s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
387s 
[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
387s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
389s 
succeeded(30)   83.3333% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
389s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
389s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
389s bt2 index files: $VAR1 = [];
389s Note - bowtie-build indices do not yet exist. Indexing genome now.
389s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
390s CMD: touch /tmp/autopkgtest.Uv0c5G/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
390s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
390s 9 reads; of these:
390s   9 (100.00%) were unpaired; of these:
390s     0 (0.00%) aligned 0 times
390s     9 (100.00%) aligned exactly 1 time
390s     0 (0.00%) aligned >1 times
390s 100.00% overall alignment rate
390s CMD: touch /tmp/autopkgtest.Uv0c5G/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
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
390s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
390s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
390s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
390s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
390s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
390s 
390s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
390s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
390s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
390s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
390s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
390s -processing jaccard pair sensor
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
390s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
391s 
succeeded(31)   86.1111% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
391s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
391s bt2 index files: $VAR1 = [];
391s Note - bowtie-build indices do not yet exist. Indexing genome now.
391s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
391s CMD: touch /tmp/autopkgtest.Uv0c5G/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
391s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
391s 20 reads; of these:
391s   20 (100.00%) were unpaired; of these:
391s     0 (0.00%) aligned 0 times
391s     20 (100.00%) aligned exactly 1 time
391s     0 (0.00%) aligned >1 times
391s 100.00% overall alignment rate
391s CMD: touch /tmp/autopkgtest.Uv0c5G/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
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
391s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
391s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
391s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
391s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
391s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
391s 
391s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
391s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
391s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
391s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
391s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
391s -processing jaccard pair sensor
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
391s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
392s 
succeeded(32)   88.8889% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
392s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
392s bt2 index files: $VAR1 = [];
392s Note - bowtie-build indices do not yet exist. Indexing genome now.
392s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
392s CMD: touch /tmp/autopkgtest.Uv0c5G/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
392s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
392s 11 reads; of these:
392s   11 (100.00%) were unpaired; of these:
392s     0 (0.00%) aligned 0 times
392s     11 (100.00%) aligned exactly 1 time
392s     0 (0.00%) aligned >1 times
392s 100.00% overall alignment rate
392s CMD: touch /tmp/autopkgtest.Uv0c5G/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
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
392s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
392s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
392s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
392s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
392s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
392s 
392s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
392s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
392s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
392s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
392s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
392s -processing jaccard pair sensor
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
392s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
393s 
succeeded(33)   91.6667% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
393s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
393s bt2 index files: $VAR1 = [];
393s Note - bowtie-build indices do not yet exist. Indexing genome now.
393s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
393s CMD: touch /tmp/autopkgtest.Uv0c5G/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
393s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
393s 9 reads; of these:
393s   9 (100.00%) were unpaired; of these:
393s     0 (0.00%) aligned 0 times
393s     9 (100.00%) aligned exactly 1 time
393s     0 (0.00%) aligned >1 times
393s 100.00% overall alignment rate
393s CMD: touch /tmp/autopkgtest.Uv0c5G/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
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
393s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
393s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
393s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
393s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
393s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
393s 
393s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
393s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
393s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
393s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
393s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
393s -processing jaccard pair sensor
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
393s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
394s 
succeeded(34)   94.4444% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
394s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
394s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
394s bt2 index files: $VAR1 = [];
394s Note - bowtie-build indices do not yet exist. Indexing genome now.
394s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
394s CMD: touch /tmp/autopkgtest.Uv0c5G/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
394s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
395s 11272 reads; of these:
395s   11272 (100.00%) were unpaired; of these:
395s     2 (0.02%) aligned 0 times
395s     1241 (11.01%) aligned exactly 1 time
395s     10029 (88.97%) aligned >1 times
395s 99.98% overall alignment rate
395s CMD: touch /tmp/autopkgtest.Uv0c5G/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
395s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
396s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
396s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
396s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
396s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
396s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
396s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
396s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
396s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
396s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
396s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
396s 
397s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
397s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
397s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
397s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
397s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
397s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
397s -processing jaccard pair sensor
398s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
398s 
[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
398s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
401s 
succeeded(35)   97.2222% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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 
401s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/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
401s bt2 index files: $VAR1 = [];
401s Note - bowtie-build indices do not yet exist. Indexing genome now.
401s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
401s CMD: touch /tmp/autopkgtest.Uv0c5G/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
401s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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" 
401s 18 reads; of these:
401s   18 (100.00%) were unpaired; of these:
401s     0 (0.00%) aligned 0 times
401s     18 (100.00%) aligned exactly 1 time
401s     0 (0.00%) aligned >1 times
401s 100.00% overall alignment rate
401s CMD: touch /tmp/autopkgtest.Uv0c5G/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
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/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
401s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/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
401s CMD: samtools index /tmp/autopkgtest.Uv0c5G/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
401s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/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
401s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
401s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
401s 
401s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
401s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
401s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
401s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
401s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
401s -processing jaccard pair sensor
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
401s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
401s 
succeeded(36)   100% completed.    
401s 
401s All commands completed successfully. :-)
401s 
401s 
401s 
401s ** Harvesting all assembled transcripts into a single multi-fasta file...
401s 
401s Wednesday, October 29, 2025: 03:50:12	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp
401s * [Wed Oct 29 03:50:12 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1
402s * [Wed Oct 29 03:50:13 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
402s Wednesday, October 29, 2025: 03:50:13	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map
402s 
402s 
402s #############################################################################
402s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
402s #############################################################################
402s 
402s 
402s 
402s 
402s exit 0
402s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
402s #!/bin/bash -ve
402s 
402s 
402s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
402s     gunzip -c reads.right.fq.gz > reads.right.fq
402s fi
402s 
402s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
402s     gunzip -c reads.left.fq.gz > reads.left.fq
402s fi
402s 
402s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
402s     gunzip -c reads2.right.fq.gz > reads2.right.fq
402s fi
402s 
402s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
402s     gunzip -c reads2.left.fq.gz > reads2.left.fq
402s fi
402s 
402s 
402s #######################################################
402s ##  Run Trinity to Generate Transcriptome Assemblies ##
402s #######################################################
402s 
402s CPU=$(nproc || sysctl -n hw.physicalcpu)
402s 
402s ${TRINITY_HOME}/Trinity --seqType fq \
402s               --max_memory 2G \
402s               --left reads.left.fq,reads2.left.fq \
402s               --right reads.right.fq,reads2.right.fq \
402s               --SS_lib_type RF \
402s               --CPU ${CPU} \
402s               --trimmomatic \
402s               --normalize_reads \
402s               --normalize_by_read_set \
402s               --output trinity_trim_and_norm_outdir
402s 
402s 
402s      ______  ____   ____  ____   ____  ______  __ __
402s     |      ||    \ |    ||    \ |    ||      ||  |  |
402s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
402s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
402s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
402s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
402s       |__|  |__|\_||____||__|__||____|  |__|  |____/
402s 
402s     Trinity-v2.15.2
402s 
402s 
402s 
402s Left read files: $VAR1 = [
402s           'reads.left.fq',
402s           'reads2.left.fq'
402s         ];
402s Right read files: $VAR1 = [
402s           'reads.right.fq',
402s           'reads2.right.fq'
402s         ];
403s Wednesday, October 29, 2025: 03:50:13	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir
403s Wednesday, October 29, 2025: 03:50:13	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis
403s 
403s 
403s ----------------------------------------------------------------------------------
403s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
403s ----------------------------------------------------------------------------------
403s 
403s ---------------------------------------------------------------
403s ------ Quality Trimming Via Trimmomatic  ---------------------
403s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
403s ---------------------------------------------------------------
403s 
403s 
403s ## Running Trimmomatic on read files: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
403s Wednesday, October 29, 2025: 03:50:13	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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 
403s TrimmomaticPE: Started with arguments:
403s  -threads 2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.Uv0c5G/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
403s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
403s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
403s Quality encoding detected as phred33
403s 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%)
403s TrimmomaticPE: Completed successfully
403s Wednesday, October 29, 2025: 03:50:13	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
403s Wednesday, October 29, 2025: 03:50:13	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
403s Wednesday, October 29, 2025: 03:50:13	CMD: touch trimmomatic.ok
403s Wednesday, October 29, 2025: 03:50:13	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
403s 
403s ## Running Trimmomatic on read files: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq
403s Wednesday, October 29, 2025: 03:50:13	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.Uv0c5G/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 
403s TrimmomaticPE: Started with arguments:
403s  -threads 2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.Uv0c5G/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
403s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
403s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
403s Quality encoding detected as phred33
404s 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%)
404s TrimmomaticPE: Completed successfully
404s Wednesday, October 29, 2025: 03:50:14	CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq
404s Wednesday, October 29, 2025: 03:50:14	CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq
404s Wednesday, October 29, 2025: 03:50:14	CMD: touch trimmomatic.ok
404s Wednesday, October 29, 2025: 03:50:14	CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim &
404s ---------------------------------------------------------------
404s ------------ In silico Read Normalization ---------------------
404s -- (Removing Excess Reads Beyond 200 Coverage --
404s ---------------------------------------------------------------
404s 
404s 
404s ## Running in silico normalization, processing each read set separately
404s # running normalization on reads: $VAR1 = [
404s           [
404s             'reads.left.fq.PwU.qtrim.fq'
404s           ],
404s           [
404s             'reads.right.fq.PwU.qtrim.fq'
404s           ]
404s         ];
404s 
404s 
404s Wednesday, October 29, 2025: 03:50:14	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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  
404s -prepping seqs
404s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa
404s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa
404s CMD finished (0 seconds)
404s CMD finished (0 seconds)
404s CMD: touch left.fa.ok
404s CMD finished (0 seconds)
404s CMD: touch right.fa.ok
404s CMD finished (0 seconds)
404s  Done converting input files. CMD: cat left.fa right.fa > both.fa
404s CMD finished (0 seconds)
404s CMD: touch both.fa.ok
404s CMD finished (0 seconds)
404s -kmer counting.
404s -------------------------------------------
404s ----------- Jellyfish  --------------------
404s -- (building a k-mer catalog from reads) --
404s -------------------------------------------
404s 
404s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
405s CMD finished (1 seconds)
405s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
405s CMD finished (0 seconds)
405s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
405s CMD finished (0 seconds)
405s CMD: touch jellyfish.K25.min2.kmers.fa.success
405s CMD finished (0 seconds)
405s -generating stats files
405s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
405s -reading Kmer occurrences...
405s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
405s -reading Kmer occurrences...
405s 
405s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
405s 
405s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
405s STATS_GENERATION_TIME: 0 seconds.
405s STATS_GENERATION_TIME: 0 seconds.
405s CMD finished (0 seconds)
405s CMD finished (0 seconds)
405s CMD: touch left.fa.K25.stats.ok
405s CMD finished (0 seconds)
405s CMD: touch right.fa.K25.stats.ok
405s CMD finished (0 seconds)
405s -sorting each stats file by read name.
405s 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
405s 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
405s CMD finished (0 seconds)
405s CMD finished (0 seconds)
405s CMD: touch left.fa.K25.stats.sort.ok
405s CMD finished (0 seconds)
405s CMD: touch right.fa.K25.stats.sort.ok
405s CMD finished (0 seconds)
405s -defining normalized reads
405s 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
405s -opening left.fa.K25.stats.sort
405s -opening right.fa.K25.stats.sort
405s -done opening files.
405s CMD finished (1 seconds)
405s CMD: touch pairs.K25.stats.ok
405s CMD finished (0 seconds)
405s 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
405s 27678 / 27726 = 99.83% reads selected during normalization.
405s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
405s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
405s CMD finished (0 seconds)
405s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
405s CMD finished (0 seconds)
405s -search and capture.
406s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
406s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq
406s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
406s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq
406s CMD: touch /tmp/autopkgtest.Uv0c5G/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
406s CMD finished (0 seconds)
406s CMD: touch /tmp/autopkgtest.Uv0c5G/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
406s CMD finished (0 seconds)
406s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
406s CMD finished (0 seconds)
406s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
406s CMD finished (0 seconds)
406s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads
406s 
406s 
406s Normalization complete. See outputs: 
406s 	/tmp/autopkgtest.Uv0c5G/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
406s 	/tmp/autopkgtest.Uv0c5G/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
406s Wednesday, October 29, 2025: 03:50:16	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok
406s # running normalization on reads: $VAR1 = [
406s           [
406s             'reads2.left.fq.PwU.qtrim.fq'
406s           ],
406s           [
406s             'reads2.right.fq.PwU.qtrim.fq'
406s           ]
406s         ];
406s 
406s 
406s Wednesday, October 29, 2025: 03:50:16	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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  
406s -prepping seqs
406s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa
406s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa
406s CMD finished (0 seconds)
406s CMD finished (0 seconds)
406s CMD: touch left.fa.ok
406s CMD finished (0 seconds)
406s CMD: touch right.fa.ok
406s CMD finished (0 seconds)
406s  Done converting input files. CMD: cat left.fa right.fa > both.fa
406s CMD finished (0 seconds)
406s CMD: touch both.fa.ok
406s CMD finished (0 seconds)
406s -kmer counting.
406s -------------------------------------------
406s ----------- Jellyfish  --------------------
406s -- (building a k-mer catalog from reads) --
406s -------------------------------------------
406s 
406s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
406s CMD finished (1 seconds)
406s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
406s CMD finished (0 seconds)
406s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
406s CMD finished (0 seconds)
406s CMD: touch jellyfish.K25.min2.kmers.fa.success
406s CMD finished (0 seconds)
406s -generating stats files
406s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
406s -reading Kmer occurrences...
406s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
406s -reading Kmer occurrences...
406s 
406s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
406s 
406s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
407s STATS_GENERATION_TIME: 0 seconds.
407s CMD finished (0 seconds)
407s STATS_GENERATION_TIME: 0 seconds.
407s CMD finished (0 seconds)
407s CMD: touch left.fa.K25.stats.ok
407s CMD finished (0 seconds)
407s CMD: touch right.fa.K25.stats.ok
407s CMD finished (0 seconds)
407s -sorting each stats file by read name.
407s 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
407s 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
407s CMD finished (0 seconds)
407s CMD finished (0 seconds)
407s CMD: touch left.fa.K25.stats.sort.ok
407s CMD finished (0 seconds)
407s CMD: touch right.fa.K25.stats.sort.ok
407s CMD finished (0 seconds)
407s -defining normalized reads
407s 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
407s -opening left.fa.K25.stats.sort
407s -opening right.fa.K25.stats.sort
407s -done opening files.
407s CMD finished (0 seconds)
407s CMD: touch pairs.K25.stats.ok
407s CMD finished (0 seconds)
407s 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
407s 27678 / 27726 = 99.83% reads selected during normalization.
407s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
407s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
407s CMD finished (0 seconds)
407s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
407s CMD finished (0 seconds)
407s -search and capture.
407s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
407s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq
407s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/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.
407s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq
407s CMD: touch /tmp/autopkgtest.Uv0c5G/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
407s CMD finished (0 seconds)
407s CMD: touch /tmp/autopkgtest.Uv0c5G/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
407s CMD finished (0 seconds)
407s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
407s CMD finished (0 seconds)
407s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
407s CMD finished (0 seconds)
407s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads
407s 
407s 
407s Normalization complete. See outputs: 
407s 	/tmp/autopkgtest.Uv0c5G/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
407s 	/tmp/autopkgtest.Uv0c5G/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
407s Wednesday, October 29, 2025: 03:50:18	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok
407s # running normalization on reads: $VAR1 = [
407s           [
407s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq',
407s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq'
407s           ],
407s           [
407s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq',
407s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq'
407s           ]
407s         ];
407s 
407s 
407s Wednesday, October 29, 2025: 03:50:18	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.Uv0c5G/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  
408s -prepping seqs
408s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa
408s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa
408s CMD finished (0 seconds)
408s CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa
408s CMD finished (0 seconds)
408s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa
408s CMD finished (0 seconds)
408s CMD finished (0 seconds)
408s CMD: touch left.fa.ok
408s CMD finished (0 seconds)
408s CMD: touch right.fa.ok
408s CMD finished (0 seconds)
408s  Done converting input files. CMD: cat left.fa right.fa > both.fa
408s CMD finished (0 seconds)
408s CMD: touch both.fa.ok
408s CMD finished (0 seconds)
408s -kmer counting.
408s -------------------------------------------
408s ----------- Jellyfish  --------------------
408s -- (building a k-mer catalog from reads) --
408s -------------------------------------------
408s 
408s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
408s CMD finished (1 seconds)
408s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
408s CMD finished (0 seconds)
408s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
408s CMD finished (0 seconds)
408s CMD: touch jellyfish.K25.min2.kmers.fa.success
408s CMD finished (0 seconds)
408s -generating stats files
408s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
408s -reading Kmer occurrences...
408s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
408s -reading Kmer occurrences...
408s 
408s  done parsing 311705 Kmers, 310319 added, taking 0 seconds.
408s 
408s  done parsing 311705 Kmers, 310319 added, taking 0 seconds.
409s STATS_GENERATION_TIME: 0 seconds.
409s STATS_GENERATION_TIME: 0 seconds.
409s CMD finished (0 seconds)
409s CMD finished (0 seconds)
409s CMD: touch left.fa.K25.stats.ok
409s CMD finished (0 seconds)
409s CMD: touch right.fa.K25.stats.ok
409s CMD finished (0 seconds)
409s -sorting each stats file by read name.
409s 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
409s 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
409s CMD finished (0 seconds)
409s CMD finished (0 seconds)
409s CMD: touch left.fa.K25.stats.sort.ok
409s CMD finished (0 seconds)
409s CMD: touch right.fa.K25.stats.sort.ok
409s CMD finished (0 seconds)
409s -defining normalized reads
409s 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
409s -opening left.fa.K25.stats.sort
409s -opening right.fa.K25.stats.sort
409s -done opening files.
409s CMD finished (1 seconds)
409s CMD: touch pairs.K25.stats.ok
409s CMD finished (0 seconds)
409s 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
410s 51602 / 55356 = 93.22% reads selected during normalization.
410s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles.
410s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1
410s CMD finished (0 seconds)
410s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
410s CMD finished (0 seconds)
410s -search and capture.
410s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.Uv0c5G/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.
410s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq
410s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq
410s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.Uv0c5G/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.
410s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq
410s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq
410s CMD: touch /tmp/autopkgtest.Uv0c5G/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
410s CMD finished (0 seconds)
410s CMD: touch /tmp/autopkgtest.Uv0c5G/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
410s CMD finished (0 seconds)
410s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
410s CMD finished (0 seconds)
410s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
410s CMD finished (0 seconds)
410s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads
410s 
410s 
410s Normalization complete. See outputs: 
410s 	/tmp/autopkgtest.Uv0c5G/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
410s 	/tmp/autopkgtest.Uv0c5G/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
410s Wednesday, October 29, 2025: 03:50:21	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok
410s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:50:21	CMD: cat /tmp/autopkgtest.Uv0c5G/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
410s Wednesday, October 29, 2025: 03:50:21	CMD: cat /tmp/autopkgtest.Uv0c5G/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
410s Wednesday, October 29, 2025: 03:50:21	CMD: touch left.fa.ok
410s Wednesday, October 29, 2025: 03:50:21	CMD: touch right.fa.ok
410s Wednesday, October 29, 2025: 03:50:21	CMD: touch left.fa.ok right.fa.ok
410s Wednesday, October 29, 2025: 03:50:21	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
410s Wednesday, October 29, 2025: 03:50:21	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok
410s -------------------------------------------
410s ----------- Jellyfish  --------------------
410s -- (building a k-mer (25) catalog from reads) --
410s -------------------------------------------
410s 
410s * [Wed Oct 29 03:50:21 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
411s * [Wed Oct 29 03:50:21 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
411s * [Wed Oct 29 03:50:21 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
411s ----------------------------------------------
411s --------------- Inchworm (K=25, asm) ---------------------
411s -- (Linear contig construction from k-mers) --
411s ----------------------------------------------
411s 
411s * [Wed Oct 29 03:50:21 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp
411s Kmer length set to: 25
411s Min assembly length set to: 25
411s Monitor turned on, set to: 1
411s min entropy set to: 1
411s setting number of threads to: 2
411s -setting parallel iworm mode.
411s -reading Kmer occurrences...
411s 
 [0M] Kmers parsed.     
411s  done parsing 309493 Kmers, 309493 added, taking 1 seconds.
411s 
411s TIMING KMER_DB_BUILDING 1 s.
411s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
411s Pruned 1482 kmers from catalog.
411s 	Pruning time: 0 seconds = 0 minutes.
411s 
411s TIMING PRUNING 0 s.
411s -populating the kmer seed candidate list.
411s Kcounter hash size: 309493
411s Processed 308011 non-zero abundance kmers in kcounter.
411s -Not sorting list of kmers, given parallel mode in effect.
411s -beginning inchworm contig assembly.
411s Total kcounter hash size: 309493 vs. sorted list size: 308011
411s num threads set to: 2
411s Done opening file. tmp.iworm.fa.pid_42925.thread_0
411s Done opening file. tmp.iworm.fa.pid_42925.thread_1
411s 
411s 	Iworm contig assembly time: 0 seconds = 0 minutes.
411s 
411s TIMING CONTIG_BUILDING 0 s.
411s 
411s TIMING PROG_RUNTIME 1 s.
411s * [Wed Oct 29 03:50:22 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa
411s Wednesday, October 29, 2025: 03:50:22	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished
411s --------------------------------------------------------
411s -------------------- Chrysalis -------------------------
411s -- (Contig Clustering & de Bruijn Graph Construction) --
411s --------------------------------------------------------
411s 
411s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
411s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
411s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
411s * [Wed Oct 29 03:50:22 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100
412s * [Wed Oct 29 03:50:22 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null
412s * [Wed Oct 29 03:50:22 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 
418s * [Wed Oct 29 03:50:28 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200
419s * [Wed Oct 29 03:50:29 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/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 
421s * [Wed Oct 29 03:50:31 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort
421s Wednesday, October 29, 2025: 03:50:31	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0
421s Wednesday, October 29, 2025: 03:50:31	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok
421s Wednesday, October 29, 2025: 03:50:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
421s Wednesday, October 29, 2025: 03:50:31	CMD: touch recursive_trinity.cmds.ok
421s Wednesday, October 29, 2025: 03:50:31	CMD: touch recursive_trinity.cmds.ok
421s 
421s 
421s --------------------------------------------------------------------------------
421s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
421s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
421s --------------------------------------------------------------------------------
421s 
421s Wednesday, October 29, 2025: 03:50:31	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
421s Number of Commands: 51
468s 
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.    
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succeeded(13)   25.4902% completed.    
succeeded(14)   27.451% completed.    
succeeded(15)   29.4118% completed.    
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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.    
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succeeded(24)   47.0588% completed.    
succeeded(25)   49.0196% completed.    
succeeded(26)   50.9804% completed.    
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succeeded(28)   54.902% completed.    
succeeded(29)   56.8627% completed.    
succeeded(30)   58.8235% completed.    
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succeeded(33)   64.7059% completed.    
succeeded(34)   66.6667% completed.    
succeeded(35)   68.6275% completed.    
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succeeded(38)   74.5098% completed.    
succeeded(39)   76.4706% completed.    
succeeded(40)   78.4314% completed.    
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succeeded(42)   82.3529% completed.    
succeeded(43)   84.3137% completed.    
succeeded(44)   86.2745% completed.    
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succeeded(46)   90.1961% completed.    
succeeded(47)   92.1569% completed.    
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succeeded(49)   96.0784% completed.    
succeeded(50)   98.0392% completed.    
succeeded(51)   100% completed.    
468s 
468s All commands completed successfully. :-)
468s 
468s 
468s 
468s ** Harvesting all assembled transcripts into a single multi-fasta file...
468s 
468s Wednesday, October 29, 2025: 03:51:19	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp
468s * [Wed Oct 29 03:51:19 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2
469s * [Wed Oct 29 03:51:19 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
469s Wednesday, October 29, 2025: 03:51:20	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map
469s 
469s 
469s #############################################################################
469s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
469s #############################################################################
469s 
469s 
469s 
469s 
469s 
469s exit 0
469s ./misc_run_tests/__runMe_include_long_reads.sh
469s #!/bin/bash -ve
469s 
469s #######################################################
469s ##  Run Trinity to Generate Transcriptome Assemblies ##
469s #######################################################
469s 
469s CPU=$(nproc || sysctl -n hw.physicalcpu)
469s 
469s ${TRINITY_HOME}/Trinity --seqType fq \
469s               --max_memory 2G \
469s               --left reads.left.fq.gz \
469s               --right reads.right.fq.gz \
469s               --SS_lib_type RF \
469s               --CPU ${CPU} \
469s               --no_cleanup \
469s               --long_reads longReads.fa \
469s               --output test_trinity_long_reads
469s 
469s 
469s      ______  ____   ____  ____   ____  ______  __ __
469s     |      ||    \ |    ||    \ |    ||      ||  |  |
469s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
469s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
469s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
469s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
469s       |__|  |__|\_||____||__|__||____|  |__|  |____/
469s 
469s     Trinity-v2.15.2
469s 
469s 
469s 
469s Left read files: $VAR1 = [
469s           'reads.left.fq.gz'
469s         ];
469s Right read files: $VAR1 = [
469s           'reads.right.fq.gz'
469s         ];
469s Wednesday, October 29, 2025: 03:51:20	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads
469s Wednesday, October 29, 2025: 03:51:20	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis
469s 
469s 
469s ----------------------------------------------------------------------------------
469s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
469s ----------------------------------------------------------------------------------
469s 
469s ---------------------------------------------------------------
469s ------------ In silico Read Normalization ---------------------
469s -- (Removing Excess Reads Beyond 200 Coverage --
469s ---------------------------------------------------------------
469s 
469s # running normalization on reads: $VAR1 = [
469s           [
469s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
469s           ],
469s           [
469s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
469s           ]
469s         ];
469s 
469s 
469s Wednesday, October 29, 2025: 03:51:20	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
469s -prepping seqs
469s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
469s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
469s CMD finished (0 seconds)
469s CMD finished (0 seconds)
469s CMD: touch left.fa.ok
469s CMD finished (0 seconds)
469s CMD: touch right.fa.ok
469s CMD finished (0 seconds)
469s  Done converting input files. CMD: cat left.fa right.fa > both.fa
469s CMD finished (0 seconds)
469s CMD: touch both.fa.ok
469s CMD finished (0 seconds)
469s -kmer counting.
469s -------------------------------------------
469s ----------- Jellyfish  --------------------
469s -- (building a k-mer catalog from reads) --
469s -------------------------------------------
469s 
469s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
470s CMD finished (0 seconds)
470s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
470s CMD finished (0 seconds)
470s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
470s CMD finished (0 seconds)
470s CMD: touch jellyfish.K25.min2.kmers.fa.success
470s CMD finished (0 seconds)
470s -generating stats files
470s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
470s -reading Kmer occurrences...
470s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
470s -reading Kmer occurrences...
470s 
470s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
470s 
470s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
470s STATS_GENERATION_TIME: 1 seconds.
470s CMD finished (1 seconds)
470s STATS_GENERATION_TIME: 1 seconds.
470s CMD finished (1 seconds)
470s CMD: touch left.fa.K25.stats.ok
470s CMD finished (0 seconds)
470s CMD: touch right.fa.K25.stats.ok
470s CMD finished (0 seconds)
470s -sorting each stats file by read name.
470s 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
470s 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
470s CMD finished (0 seconds)
470s CMD finished (0 seconds)
470s CMD: touch left.fa.K25.stats.sort.ok
471s CMD finished (0 seconds)
471s CMD: touch right.fa.K25.stats.sort.ok
471s CMD finished (0 seconds)
471s -defining normalized reads
471s 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
471s -opening left.fa.K25.stats.sort
471s -opening right.fa.K25.stats.sort
471s -done opening files.
471s CMD finished (0 seconds)
471s CMD: touch pairs.K25.stats.ok
471s CMD finished (0 seconds)
471s 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
471s 30472 / 30575 = 99.66% reads selected during normalization.
471s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
471s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
471s CMD finished (0 seconds)
471s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
471s CMD finished (0 seconds)
471s -search and capture.
471s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
471s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
471s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
471s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
471s CMD: touch /tmp/autopkgtest.Uv0c5G/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
471s CMD finished (0 seconds)
471s CMD: touch /tmp/autopkgtest.Uv0c5G/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
471s CMD finished (0 seconds)
471s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
471s CMD finished (0 seconds)
471s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
471s CMD finished (0 seconds)
471s 
471s 
471s Normalization complete. See outputs: 
471s 	/tmp/autopkgtest.Uv0c5G/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
471s 	/tmp/autopkgtest.Uv0c5G/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
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok
471s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:51:22	CMD: cat /tmp/autopkgtest.Uv0c5G/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
471s Wednesday, October 29, 2025: 03:51:22	CMD: cat /tmp/autopkgtest.Uv0c5G/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
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch right.fa.ok
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch left.fa.ok
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch left.fa.ok right.fa.ok
471s Wednesday, October 29, 2025: 03:51:22	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok
471s Wednesday, October 29, 2025: 03:51:22	CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
471s Wednesday, October 29, 2025: 03:51:22	CMD: cat /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
471s Wednesday, October 29, 2025: 03:51:22	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok
471s -------------------------------------------
471s ----------- Jellyfish  --------------------
471s -- (building a k-mer (25) catalog from reads) --
471s -------------------------------------------
471s 
471s * [Wed Oct 29 03:51:22 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
472s * [Wed Oct 29 03:51:22 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
472s * [Wed Oct 29 03:51:22 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
472s ----------------------------------------------
472s --------------- Inchworm (K=25, asm) ---------------------
472s -- (Linear contig construction from k-mers) --
472s ----------------------------------------------
472s 
472s * [Wed Oct 29 03:51:22 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp
472s Kmer length set to: 25
472s Min assembly length set to: 25
472s Monitor turned on, set to: 1
472s -retaining tmp files
472s min entropy set to: 1
472s setting number of threads to: 2
472s -setting parallel iworm mode.
472s -reading Kmer occurrences...
472s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
472s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
472s 
472s TIMING KMER_DB_BUILDING 1 s.
472s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
472s Pruned 4252 kmers from catalog.
472s 	Pruning time: 0 seconds = 0 minutes.
472s 
472s TIMING PRUNING 0 s.
472s -populating the kmer seed candidate list.
472s Kcounter hash size: 519541
472s Processed 515289 non-zero abundance kmers in kcounter.
472s -Not sorting list of kmers, given parallel mode in effect.
472s -beginning inchworm contig assembly.
472s Total kcounter hash size: 519541 vs. sorted list size: 515289
472s num threads set to: 2
472s Done opening file. tmp.iworm.fa.pid_51980.thread_0
472s Done opening file. tmp.iworm.fa.pid_51980.thread_1
473s 
473s 	Iworm contig assembly time: 0 seconds = 0 minutes.
473s 
473s TIMING CONTIG_BUILDING 0 s.
473s 
473s TIMING PROG_RUNTIME 1 s.
473s * [Wed Oct 29 03:51:23 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa
473s Wednesday, October 29, 2025: 03:51:23	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished
473s --------------------------------------------------------
473s -------------------- Chrysalis -------------------------
473s -- (Contig Clustering & de Bruijn Graph Construction) --
473s --------------------------------------------------------
473s 
473s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
473s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
473s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
473s * [Wed Oct 29 03:51:23 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100
473s * [Wed Oct 29 03:51:23 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null
473s * [Wed Oct 29 03:51:23 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 
476s * [Wed Oct 29 03:51:26 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt
476s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt
477s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted
477s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
477s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out
477s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200
477s * [Wed Oct 29 03:51:27 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
478s * [Wed Oct 29 03:51:28 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort
478s Wednesday, October 29, 2025: 03:51:28	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0
478s Wednesday, October 29, 2025: 03:51:28	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok
478s Wednesday, October 29, 2025: 03:51:28	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
478s Wednesday, October 29, 2025: 03:51:28	CMD: touch recursive_trinity.cmds.ok
478s Wednesday, October 29, 2025: 03:51:28	CMD: touch recursive_trinity.cmds.ok
478s 
478s 
478s --------------------------------------------------------------------------------
478s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
478s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
478s --------------------------------------------------------------------------------
478s 
478s Wednesday, October 29, 2025: 03:51:28	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
478s Number of Commands: 38
509s 
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.    
509s 
509s All commands completed successfully. :-)
509s 
509s 
509s 
509s ** Harvesting all assembled transcripts into a single multi-fasta file...
509s 
509s Wednesday, October 29, 2025: 03:51:59	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp
509s * [Wed Oct 29 03:51:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2
509s * [Wed Oct 29 03:51:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
509s Wednesday, October 29, 2025: 03:51:59	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map
509s 
509s 
509s #############################################################################
509s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
509s #############################################################################
509s 
509s 
509s 
509s 
509s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta"  -exec cat {} \; | grep LR
509s >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(-)]}
509s >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$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
509s >c0_g1_i2 len=1946 path=[1:0-219 198:220-220 199:221-304 283:305-325 304:326-1945] [-1, 1, 198, 199, 283, 304, -2] long_read_mappings: {PairPath [_paths=[[1, 198, 199, 283, 304], []]]=[LR$|mm9chr9-NM_026942;mm9chr9-69106_Stoml1_stomatin-like_1_mm9chr9:58101074-58109646(+)]}
509s >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$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]}
509s >c0_g1_i2 len=4179 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 5684:4165-4178] [-1, 1, 1730, 1752, 2672, 5684, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
509s >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$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
509s >c0_g1_i1 len=6205 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 7380:6204-6204] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 7380, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
509s >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$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
509s >c0_g1_i5 len=7194 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 6182:6204-6219 6198:6220-6729 6708:6730-6733 6712:6734-6735 6714:6736-7193] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 6182, 6198, 6708, 6712, 6714, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
509s >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$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]}
509s >c0_g1_i3 len=2433 path=[1:0-610 589:611-1077 2766:1078-1168 1078:1169-1610 1520:1611-1690 1600:1691-1863 1773:1864-2097 2007:2098-2098 2008:2099-2432] [-1, 1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
509s >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, 10
509s 
509s exit 0
509s #!/bin/bash -ve
509s 
509s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
509s               --seqType fq \
509s               --max_memory 1G \
509s               --output trinity_test_samples_PE
509s 56, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
509s >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$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
509s >c0_g3_i8 len=8757 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 7602:7624-7968 7947:7969-7969 7948:7970-7982 7961:7983-7983 7962:7984-8252 8231:8253-8747 8726:8748-8756] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 7602, 7947, 7948, 7961, 7962, 8231, 8726, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
509s >c0_g2_i8 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$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
509s >c0_g2_i16 len=2273 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 6207:2249-2272] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 6207, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
509s >c0_g2_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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
509s >c0_g2_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
509s >c0_g2_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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
509s >c0_g2_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
509s ./misc_run_tests/__run_PE_samples_file.sh
509s 
509s 
509s      ______  ____   ____  ____   ____  ______  __ __
509s     |      ||    \ |    ||    \ |    ||      ||  |  |
509s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
509s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
509s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
509s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
509s       |__|  |__|\_||____||__|__||____|  |__|  |____/
509s 
509s     Trinity-v2.15.2
509s 
509s 
509s 
509s Left read files: $VAR1 = [
509s           'reads.left.fq.gz',
509s           'reads2.left.fq.gz'
509s         ];
509s Right read files: $VAR1 = [
509s           'reads.right.fq.gz',
509s           'reads2.right.fq.gz'
509s         ];
509s Wednesday, October 29, 2025: 03:51:59	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE
509s Wednesday, October 29, 2025: 03:51:59	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis
509s 
509s 
509s ----------------------------------------------------------------------------------
509s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
509s ----------------------------------------------------------------------------------
509s 
509s ---------------------------------------------------------------
509s ------------ In silico Read Normalization ---------------------
509s -- (Removing Excess Reads Beyond 200 Coverage --
509s ---------------------------------------------------------------
509s 
509s # running normalization on reads: $VAR1 = [
509s           [
509s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
509s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
509s           ],
509s           [
509s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
509s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
509s           ]
509s         ];
509s 
509s 
509s Wednesday, October 29, 2025: 03:51:59	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
509s -prepping seqs
509s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
509s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
509s CMD finished (0 seconds)
509s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
509s CMD finished (0 seconds)
509s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
509s CMD finished (0 seconds)
509s CMD finished (0 seconds)
509s CMD: touch left.fa.ok
509s CMD finished (0 seconds)
509s CMD: touch right.fa.ok
509s CMD finished (0 seconds)
509s  Done converting input files. CMD: cat left.fa right.fa > both.fa
509s CMD finished (0 seconds)
509s CMD: touch both.fa.ok
509s CMD finished (0 seconds)
509s -kmer counting.
509s -------------------------------------------
509s ----------- Jellyfish  --------------------
509s -- (building a k-mer catalog from reads) --
509s -------------------------------------------
509s 
509s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
510s CMD finished (1 seconds)
510s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
510s CMD finished (0 seconds)
510s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
510s CMD finished (0 seconds)
510s CMD: touch jellyfish.K25.min2.kmers.fa.success
510s CMD finished (0 seconds)
510s -generating stats files
510s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
510s -reading Kmer occurrences...
510s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
510s -reading Kmer occurrences...
510s 
510s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
510s 
510s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
511s STATS_GENERATION_TIME: 0 seconds.
511s STATS_GENERATION_TIME: 0 seconds.
511s CMD finished (1 seconds)
511s CMD finished (1 seconds)
511s CMD: touch left.fa.K25.stats.ok
511s CMD finished (0 seconds)
511s CMD: touch right.fa.K25.stats.ok
511s CMD finished (0 seconds)
511s -sorting each stats file by read name.
511s 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
511s 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
511s CMD finished (0 seconds)
511s CMD finished (0 seconds)
511s CMD: touch left.fa.K25.stats.sort.ok
511s CMD finished (0 seconds)
511s CMD: touch right.fa.K25.stats.sort.ok
511s CMD finished (0 seconds)
511s -defining normalized reads
511s 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
511s -opening left.fa.K25.stats.sort
511s -opening right.fa.K25.stats.sort
511s -done opening files.
511s CMD finished (1 seconds)
511s CMD: touch pairs.K25.stats.ok
511s CMD finished (0 seconds)
511s 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
512s 56508 / 61150 = 92.41% reads selected during normalization.
512s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
512s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
512s CMD finished (0 seconds)
512s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
512s CMD finished (0 seconds)
512s -search and capture.
512s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
512s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
512s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
512s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
512s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
512s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
512s CMD: touch /tmp/autopkgtest.Uv0c5G/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
512s CMD finished (0 seconds)
512s CMD: touch /tmp/autopkgtest.Uv0c5G/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
512s CMD finished (0 seconds)
512s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
512s CMD finished (0 seconds)
512s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
512s CMD finished (0 seconds)
512s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads
512s 
512s 
512s Normalization complete. See outputs: 
512s 	/tmp/autopkgtest.Uv0c5G/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
512s 	/tmp/autopkgtest.Uv0c5G/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
512s Wednesday, October 29, 2025: 03:52:03	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok
512s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:52:03	CMD: cat /tmp/autopkgtest.Uv0c5G/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
512s Wednesday, October 29, 2025: 03:52:03	CMD: cat /tmp/autopkgtest.Uv0c5G/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
513s Wednesday, October 29, 2025: 03:52:03	CMD: touch left.fa.ok
513s Wednesday, October 29, 2025: 03:52:03	CMD: touch right.fa.ok
513s Wednesday, October 29, 2025: 03:52:03	CMD: touch left.fa.ok right.fa.ok
513s Wednesday, October 29, 2025: 03:52:03	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
513s Wednesday, October 29, 2025: 03:52:03	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok
513s -------------------------------------------
513s ----------- Jellyfish  --------------------
513s -- (building a k-mer (25) catalog from reads) --
513s -------------------------------------------
513s 
513s * [Wed Oct 29 03:52:03 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
513s * [Wed Oct 29 03:52:04 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
513s * [Wed Oct 29 03:52:04 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
513s ----------------------------------------------
513s --------------- Inchworm (K=25, asm) ---------------------
513s -- (Linear contig construction from k-mers) --
513s ----------------------------------------------
513s 
513s * [Wed Oct 29 03:52:04 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp
513s Kmer length set to: 25
513s Min assembly length set to: 25
513s Monitor turned on, set to: 1
513s double stranded mode set
513s min entropy set to: 1
513s setting number of threads to: 2
513s -setting parallel iworm mode.
513s -reading Kmer occurrences...
514s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
514s  done parsing 515206 Kmers, 515206 added, taking 0 seconds.
514s 
514s TIMING KMER_DB_BUILDING 0 s.
514s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
514s Pruned 4139 kmers from catalog.
514s 	Pruning time: 0 seconds = 0 minutes.
514s 
514s TIMING PRUNING 0 s.
514s -populating the kmer seed candidate list.
514s Kcounter hash size: 515206
514s Processed 511067 non-zero abundance kmers in kcounter.
514s -Not sorting list of kmers, given parallel mode in effect.
514s -beginning inchworm contig assembly.
514s Total kcounter hash size: 515206 vs. sorted list size: 511067
514s num threads set to: 2
514s Done opening file. tmp.iworm.fa.pid_59060.thread_0
514s Done opening file. tmp.iworm.fa.pid_59060.thread_1
514s 
514s 	Iworm contig assembly time: 0 seconds = 0 minutes.
514s 
514s TIMING CONTIG_BUILDING 0 s.
514s 
514s TIMING PROG_RUNTIME 0 s.
514s * [Wed Oct 29 03:52:05 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa
514s Wednesday, October 29, 2025: 03:52:05	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished
514s --------------------------------------------------------
514s -------------------- Chrysalis -------------------------
514s -- (Contig Clustering & de Bruijn Graph Construction) --
514s --------------------------------------------------------
514s 
514s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
514s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
514s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
514s * [Wed Oct 29 03:52:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100
514s * [Wed Oct 29 03:52:05 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null
515s * [Wed Oct 29 03:52:05 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 
521s * [Wed Oct 29 03:52:11 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt
522s * [Wed Oct 29 03:52:12 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt
523s * [Wed Oct 29 03:52:13 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted
523s * [Wed Oct 29 03:52:13 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
523s * [Wed Oct 29 03:52:13 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out
523s * [Wed Oct 29 03:52:13 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200
523s * [Wed Oct 29 03:52:13 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
526s * [Wed Oct 29 03:52:17 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort
526s Wednesday, October 29, 2025: 03:52:17	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0
527s Wednesday, October 29, 2025: 03:52:17	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok
527s Wednesday, October 29, 2025: 03:52:17	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
527s Wednesday, October 29, 2025: 03:52:17	CMD: touch recursive_trinity.cmds.ok
527s Wednesday, October 29, 2025: 03:52:17	CMD: touch recursive_trinity.cmds.ok
527s 
527s 
527s --------------------------------------------------------------------------------
527s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
527s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
527s --------------------------------------------------------------------------------
527s 
527s Wednesday, October 29, 2025: 03:52:17	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
527s Number of Commands: 61
588s 
succeeded(1)   1.63934% completed.    
succeeded(2)   3.27869% completed.    
succeeded(3)   4.91803% completed.    
succeeded(4)   6.55738% completed.    
succeeded(5)   8.19672% completed.    
succeeded(6)   9.83607% completed.    
succeeded(7)   11.4754% completed.    
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succeeded(60)   98.3607% completed.    
succeeded(61)   100% completed.    
588s 
588s All commands completed successfully. :-)
588s 
588s 
588s 
588s ** Harvesting all assembled transcripts into a single multi-fasta file...
588s 
588s Wednesday, October 29, 2025: 03:53:18	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp
588s * [Wed Oct 29 03:53:18 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2
589s * [Wed Oct 29 03:53:19 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
589s Wednesday, October 29, 2025: 03:53:19	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map
589s 
589s 
589s #############################################################################
589s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
589s #############################################################################
589s 
589s 
589s 
589s exit 0
589s ./misc_run_tests/__run_SE_samples_file.sh
589s #!/bin/bash -ve
589s 
589s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \
589s               --seqType fq \
589s               --max_memory 1G \
589s               --output trinity_test_samples_SE
589s 
589s 
589s      ______  ____   ____  ____   ____  ______  __ __
589s     |      ||    \ |    ||    \ |    ||      ||  |  |
589s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
589s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
589s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
589s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
589s       |__|  |__|\_||____||__|__||____|  |__|  |____/
589s 
589s     Trinity-v2.15.2
589s 
589s 
589s 
589s Single read files: $VAR1 = [
589s           'reads.left.fq.gz',
589s           'reads2.left.fq.gz'
589s         ];
589s Wednesday, October 29, 2025: 03:53:19	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE
589s Wednesday, October 29, 2025: 03:53:19	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis
589s 
589s 
589s ----------------------------------------------------------------------------------
589s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
589s ----------------------------------------------------------------------------------
589s 
589s ---------------------------------------------------------------
589s ------------ In silico Read Normalization ---------------------
589s -- (Removing Excess Reads Beyond 200 Coverage --
589s ---------------------------------------------------------------
589s 
589s # running normalization on reads: $VAR1 = [
589s           [
589s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
589s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
589s           ]
589s         ];
589s 
589s 
589s Wednesday, October 29, 2025: 03:53:19	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000  --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
589s -prepping seqs
589s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa
589s CMD finished (1 seconds)
589s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa
589s CMD finished (0 seconds)
589s CMD: touch single.fa.ok
589s CMD finished (0 seconds)
589s -kmer counting.
589s -------------------------------------------
589s ----------- Jellyfish  --------------------
589s -- (building a k-mer catalog from reads) --
589s -------------------------------------------
589s 
589s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
590s CMD finished (0 seconds)
590s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
590s CMD finished (0 seconds)
590s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
590s CMD finished (0 seconds)
590s CMD: touch jellyfish.K25.min2.kmers.fa.success
590s CMD finished (0 seconds)
590s -generating stats files
590s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
590s -reading Kmer occurrences...
590s 
590s  done parsing 288470 Kmers, 288470 added, taking 0 seconds.
590s STATS_GENERATION_TIME: 1 seconds.
590s CMD finished (1 seconds)
590s CMD: touch single.fa.K25.stats.ok
590s CMD finished (0 seconds)
590s -sorting each stats file by read name.
590s 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
590s CMD finished (0 seconds)
590s CMD: touch single.fa.K25.stats.sort.ok
590s CMD finished (0 seconds)
590s -defining normalized reads
590s 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
591s 59311 / 61150 = 96.99% reads selected during normalization.
591s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
591s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
591s CMD finished (0 seconds)
591s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok
591s CMD finished (0 seconds)
591s -search and capture.
591s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
591s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
591s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
591s CMD: touch /tmp/autopkgtest.Uv0c5G/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
591s CMD finished (0 seconds)
591s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
591s CMD finished (0 seconds)
591s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads
591s 
591s 
591s Normalization complete. See outputs: 
591s 	/tmp/autopkgtest.Uv0c5G/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
591s Wednesday, October 29, 2025: 03:53:22	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok
591s Wednesday, October 29, 2025: 03:53:22	CMD: cat /tmp/autopkgtest.Uv0c5G/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
591s Wednesday, October 29, 2025: 03:53:22	CMD: touch single.fa.ok
591s Wednesday, October 29, 2025: 03:53:22	CMD: touch single.fa.ok
591s -------------------------------------------
591s ----------- Jellyfish  --------------------
591s -- (building a k-mer (25) catalog from reads) --
591s -------------------------------------------
591s 
591s * [Wed Oct 29 03:53:22 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
592s * [Wed Oct 29 03:53:22 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
592s * [Wed Oct 29 03:53:22 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
592s ----------------------------------------------
592s --------------- Inchworm (K=25, asm) ---------------------
592s -- (Linear contig construction from k-mers) --
592s ----------------------------------------------
592s 
592s * [Wed Oct 29 03:53:22 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp
592s Kmer length set to: 25
592s Min assembly length set to: 25
592s Monitor turned on, set to: 1
592s double stranded mode set
592s min entropy set to: 1
592s setting number of threads to: 2
592s -setting parallel iworm mode.
592s -reading Kmer occurrences...
592s 
 [0M] Kmers parsed.     
592s  done parsing 287930 Kmers, 287930 added, taking 0 seconds.
592s 
592s TIMING KMER_DB_BUILDING 0 s.
592s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
592s Pruned 2078 kmers from catalog.
592s 	Pruning time: 0 seconds = 0 minutes.
592s 
592s TIMING PRUNING 0 s.
592s -populating the kmer seed candidate list.
592s Kcounter hash size: 287930
592s Processed 285852 non-zero abundance kmers in kcounter.
592s -Not sorting list of kmers, given parallel mode in effect.
592s -beginning inchworm contig assembly.
592s Total kcounter hash size: 287930 vs. sorted list size: 285852
592s num threads set to: 2
592s Done opening file. tmp.iworm.fa.pid_69417.thread_0
592s Done opening file. tmp.iworm.fa.pid_69417.thread_1
592s 
592s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
592s 
592s TIMING CONTIG_BUILDING 1 s.
592s 
592s TIMING PROG_RUNTIME 1 s.
592s * [Wed Oct 29 03:53:23 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa
592s Wednesday, October 29, 2025: 03:53:23	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished
592s --------------------------------------------------------
592s -------------------- Chrysalis -------------------------
592s -- (Contig Clustering & de Bruijn Graph Construction) --
592s --------------------------------------------------------
592s 
592s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
592s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
592s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
592s * [Wed Oct 29 03:53:23 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100
592s * [Wed Oct 29 03:53:23 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt
593s * [Wed Oct 29 03:53:24 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted
593s * [Wed Oct 29 03:53:24 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
593s * [Wed Oct 29 03:53:24 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out
593s * [Wed Oct 29 03:53:24 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200
593s * [Wed Oct 29 03:53:24 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
595s * [Wed Oct 29 03:53:25 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort
595s Wednesday, October 29, 2025: 03:53:25	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0
595s Wednesday, October 29, 2025: 03:53:25	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok
595s Wednesday, October 29, 2025: 03:53:25	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
595s Wednesday, October 29, 2025: 03:53:25	CMD: touch recursive_trinity.cmds.ok
595s Wednesday, October 29, 2025: 03:53:25	CMD: touch recursive_trinity.cmds.ok
595s 
595s 
595s --------------------------------------------------------------------------------
595s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
595s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
595s --------------------------------------------------------------------------------
595s 
595s Wednesday, October 29, 2025: 03:53:25	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
595s Number of Commands: 45
630s 
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.    
630s 
630s All commands completed successfully. :-)
630s 
630s 
630s 
630s ** Harvesting all assembled transcripts into a single multi-fasta file...
630s 
630s Wednesday, October 29, 2025: 03:54:00	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp
630s * [Wed Oct 29 03:54:00 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2
630s * [Wed Oct 29 03:54:01 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
630s Wednesday, October 29, 2025: 03:54:01	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map
630s 
630s 
630s #############################################################################
630s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
630s #############################################################################
630s 
630s 
630s ./misc_run_tests/__runMe_use_workdir.sh
630s 
630s 
630s exit 0
630s #!/bin/bash -ve
630s 
630s 
630s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
630s     gunzip -c reads.right.fq.gz > reads.right.fq
630s fi
630s 
630s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
630s     gunzip -c reads.left.fq.gz > reads.left.fq
630s fi
630s 
630s 
630s 
630s #######################################################
630s ##  Run Trinity to Generate Transcriptome Assemblies ##
630s #######################################################
630s 
630s CPU=$(nproc || sysctl -n hw.physicalcpu)
630s 
630s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
630s               --left reads.left.fq \
630s               --right reads.right.fq \
630s               --SS_lib_type RF \
630s               --CPU ${CPU}\
630s               --output trinity_with_workdir \
630s               --workdir  /tmp/trinity.workdir.$$ --full_cleanup
631s 
631s 
631s      ______  ____   ____  ____   ____  ______  __ __
631s     |      ||    \ |    ||    \ |    ||      ||  |  |
631s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
631s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
631s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
631s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
631s       |__|  |__|\_||____||__|__||____|  |__|  |____/
631s 
631s     Trinity-v2.15.2
631s 
631s 
631s 
631s Left read files: $VAR1 = [
631s           'reads.left.fq'
631s         ];
631s Right read files: $VAR1 = [
631s           'reads.right.fq'
631s         ];
631s Wednesday, October 29, 2025: 03:54:01	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir
631s Wednesday, October 29, 2025: 03:54:01	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis
631s 
631s 
631s ----------------------------------------------------------------------------------
631s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
631s ----------------------------------------------------------------------------------
631s 
631s ---------------------------------------------------------------
631s ------------ In silico Read Normalization ---------------------
631s -- (Removing Excess Reads Beyond 200 Coverage --
631s ---------------------------------------------------------------
631s 
631s # running normalization on reads: $VAR1 = [
631s           [
631s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq'
631s           ],
631s           [
631s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq'
631s           ]
631s         ];
631s 
631s 
631s Wednesday, October 29, 2025: 03:54:01	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together  --PARALLEL_STATS  
631s -prepping seqs
631s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa
631s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa
631s CMD finished (0 seconds)
631s CMD finished (0 seconds)
631s CMD: touch left.fa.ok
631s CMD finished (0 seconds)
631s CMD: touch right.fa.ok
631s CMD finished (0 seconds)
631s  Done converting input files. CMD: cat left.fa right.fa > both.fa
631s CMD finished (0 seconds)
631s CMD: touch both.fa.ok
631s CMD finished (0 seconds)
631s -kmer counting.
631s -------------------------------------------
631s ----------- Jellyfish  --------------------
631s -- (building a k-mer catalog from reads) --
631s -------------------------------------------
631s 
631s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
631s CMD finished (1 seconds)
631s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
631s CMD finished (0 seconds)
631s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
631s CMD finished (0 seconds)
631s CMD: touch jellyfish.K25.min2.kmers.fa.success
631s CMD finished (0 seconds)
631s -generating stats files
631s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
631s -reading Kmer occurrences...
631s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
631s -reading Kmer occurrences...
631s 
631s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
631s 
631s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
632s STATS_GENERATION_TIME: 0 seconds.
632s CMD finished (0 seconds)
632s STATS_GENERATION_TIME: 0 seconds.
632s CMD finished (0 seconds)
632s CMD: touch left.fa.K25.stats.ok
632s CMD finished (0 seconds)
632s CMD: touch right.fa.K25.stats.ok
632s CMD finished (0 seconds)
632s -sorting each stats file by read name.
632s 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
632s 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
632s CMD finished (0 seconds)
632s CMD finished (0 seconds)
632s CMD: touch left.fa.K25.stats.sort.ok
632s CMD finished (0 seconds)
632s CMD: touch right.fa.K25.stats.sort.ok
632s CMD finished (0 seconds)
632s -defining normalized reads
632s 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
632s -opening left.fa.K25.stats.sort
632s -opening right.fa.K25.stats.sort
632s -done opening files.
632s CMD finished (0 seconds)
632s CMD: touch pairs.K25.stats.ok
632s CMD finished (0 seconds)
632s 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
632s 30472 / 30575 = 99.66% reads selected during normalization.
632s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
632s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
632s CMD finished (0 seconds)
632s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
632s CMD finished (0 seconds)
632s -search and capture.
632s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture.
632s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq
632s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture.
632s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
632s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
632s CMD finished (0 seconds)
632s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
632s CMD finished (0 seconds)
632s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
632s CMD finished (0 seconds)
632s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
632s CMD finished (0 seconds)
632s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads
632s 
632s 
632s Normalization complete. See outputs: 
632s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
632s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
632s Wednesday, October 29, 2025: 03:54:03	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok
632s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:54:03	CMD: cat /tmp/autopkgtest.Uv0c5G/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
632s Wednesday, October 29, 2025: 03:54:03	CMD: cat /tmp/autopkgtest.Uv0c5G/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
632s Wednesday, October 29, 2025: 03:54:03	CMD: touch right.fa.ok
632s Wednesday, October 29, 2025: 03:54:03	CMD: touch left.fa.ok
632s Wednesday, October 29, 2025: 03:54:03	CMD: touch left.fa.ok right.fa.ok
632s Wednesday, October 29, 2025: 03:54:03	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
632s Wednesday, October 29, 2025: 03:54:03	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok
632s -------------------------------------------
632s ----------- Jellyfish  --------------------
632s -- (building a k-mer (25) catalog from reads) --
632s -------------------------------------------
632s 
632s * [Wed Oct 29 03:54:03 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
633s * [Wed Oct 29 03:54:03 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
633s * [Wed Oct 29 03:54:03 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
633s ----------------------------------------------
633s --------------- Inchworm (K=25, asm) ---------------------
633s -- (Linear contig construction from k-mers) --
633s ----------------------------------------------
633s 
633s * [Wed Oct 29 03:54:03 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp
633s Kmer length set to: 25
633s Min assembly length set to: 25
633s Monitor turned on, set to: 1
633s min entropy set to: 1
633s setting number of threads to: 2
633s -setting parallel iworm mode.
633s -reading Kmer occurrences...
633s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
633s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
633s 
633s TIMING KMER_DB_BUILDING 1 s.
633s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
633s Pruned 4252 kmers from catalog.
633s 	Pruning time: 0 seconds = 0 minutes.
633s 
633s TIMING PRUNING 0 s.
633s -populating the kmer seed candidate list.
633s Kcounter hash size: 519541
633s Processed 515289 non-zero abundance kmers in kcounter.
633s -Not sorting list of kmers, given parallel mode in effect.
633s -beginning inchworm contig assembly.
633s Total kcounter hash size: 519541 vs. sorted list size: 515289
633s num threads set to: 2
633s Done opening file. tmp.iworm.fa.pid_76422.thread_0
633s Done opening file. tmp.iworm.fa.pid_76422.thread_1
634s 
634s 	Iworm contig assembly time: 0 seconds = 0 minutes.
634s 
634s TIMING CONTIG_BUILDING 0 s.
634s 
634s TIMING PROG_RUNTIME 1 s.
634s * [Wed Oct 29 03:54:04 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa
634s Wednesday, October 29, 2025: 03:54:04	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished
634s --------------------------------------------------------
634s -------------------- Chrysalis -------------------------
634s -- (Contig Clustering & de Bruijn Graph Construction) --
634s --------------------------------------------------------
634s 
634s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
634s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
634s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
634s * [Wed Oct 29 03:54:04 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100
634s * [Wed Oct 29 03:54:04 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null
634s * [Wed Oct 29 03:54:04 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 
636s * [Wed Oct 29 03:54:06 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt
636s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt
637s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
637s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
637s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out
637s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200
637s * [Wed Oct 29 03:54:07 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
638s * [Wed Oct 29 03:54:08 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort
638s Wednesday, October 29, 2025: 03:54:08	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0
638s Wednesday, October 29, 2025: 03:54:08	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok
638s Wednesday, October 29, 2025: 03:54:08	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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.76277  --no_salmon  > recursive_trinity.cmds
638s Wednesday, October 29, 2025: 03:54:08	CMD: touch recursive_trinity.cmds.ok
638s Wednesday, October 29, 2025: 03:54:08	CMD: touch recursive_trinity.cmds.ok
638s 
638s 
638s --------------------------------------------------------------------------------
638s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
638s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
638s --------------------------------------------------------------------------------
638s 
638s Wednesday, October 29, 2025: 03:54:08	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
638s Number of Commands: 38
672s 
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.    
672s 
672s All commands completed successfully. :-)
672s 
672s 
672s 
672s ** Harvesting all assembled transcripts into a single multi-fasta file...
672s 
672s Wednesday, October 29, 2025: 03:54:42	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp
672s * [Wed Oct 29 03:54:42 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2
673s * [Wed Oct 29 03:54:43 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
673s 
673s 
673s #############################################################################
673s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
673s #############################################################################
673s 
673s 
673s Wednesday, October 29, 2025: 03:54:43	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map
673s 
673s 
673s exit 0
673s ./misc_run_tests/__runMe_piecemeal.sh
673s #!/bin/bash -ve
673s 
673s #######################################################
673s ##  Run Trinity to Generate Transcriptome Assemblies ##
673s #######################################################
673s 
673s CPU=$(nproc || sysctl -n hw.physicalcpu)
673s 
673s # stop before inchworm (just in silico norm)
673s ${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
673s 
673s 
673s      ______  ____   ____  ____   ____  ______  __ __
673s     |      ||    \ |    ||    \ |    ||      ||  |  |
673s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
673s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
673s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
673s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
673s       |__|  |__|\_||____||__|__||____|  |__|  |____/
673s 
673s     Trinity-v2.15.2
673s 
673s 
673s 
673s Left read files: $VAR1 = [
673s           'reads.left.fq.gz'
673s         ];
673s Right read files: $VAR1 = [
673s           'reads.right.fq.gz'
673s         ];
673s Wednesday, October 29, 2025: 03:54:44	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal
673s Wednesday, October 29, 2025: 03:54:44	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis
673s 
673s 
673s ----------------------------------------------------------------------------------
673s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
673s ----------------------------------------------------------------------------------
673s 
673s ---------------------------------------------------------------
673s ------------ In silico Read Normalization ---------------------
673s -- (Removing Excess Reads Beyond 200 Coverage --
673s ---------------------------------------------------------------
673s 
673s # running normalization on reads: $VAR1 = [
673s           [
673s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
673s           ],
673s           [
673s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
673s           ]
673s         ];
673s 
673s 
673s Wednesday, October 29, 2025: 03:54:44	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
673s -prepping seqs
673s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
673s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
673s CMD finished (0 seconds)
673s CMD finished (0 seconds)
673s CMD: touch left.fa.ok
673s CMD finished (0 seconds)
673s CMD: touch right.fa.ok
673s CMD finished (0 seconds)
673s  Done converting input files. CMD: cat left.fa right.fa > both.fa
673s CMD finished (0 seconds)
673s CMD: touch both.fa.ok
673s CMD finished (0 seconds)
673s -kmer counting.
673s -------------------------------------------
673s ----------- Jellyfish  --------------------
673s -- (building a k-mer catalog from reads) --
673s -------------------------------------------
673s 
673s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
674s CMD finished (0 seconds)
674s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
674s CMD finished (0 seconds)
674s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
674s CMD finished (0 seconds)
674s CMD: touch jellyfish.K25.min2.kmers.fa.success
674s CMD finished (0 seconds)
674s -generating stats files
674s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
674s -reading Kmer occurrences...
674s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
674s -reading Kmer occurrences...
674s 
674s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
674s 
674s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
674s STATS_GENERATION_TIME: 1 seconds.
674s STATS_GENERATION_TIME: 1 seconds.
674s CMD finished (1 seconds)
674s CMD finished (1 seconds)
674s CMD: touch left.fa.K25.stats.ok
674s CMD finished (0 seconds)
674s CMD: touch right.fa.K25.stats.ok
674s CMD finished (0 seconds)
674s -sorting each stats file by read name.
674s 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
674s 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
674s CMD finished (0 seconds)
674s CMD finished (0 seconds)
674s CMD: touch left.fa.K25.stats.sort.ok
674s CMD finished (0 seconds)
674s CMD: touch right.fa.K25.stats.sort.ok
674s CMD finished (0 seconds)
674s -defining normalized reads
674s 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
674s -opening left.fa.K25.stats.sort
674s -opening right.fa.K25.stats.sort
674s -done opening files.
675s CMD finished (0 seconds)
675s CMD: touch pairs.K25.stats.ok
675s CMD finished (0 seconds)
675s 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
675s 30472 / 30575 = 99.66% reads selected during normalization.
675s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
675s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
675s CMD finished (0 seconds)
675s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
675s CMD finished (0 seconds)
675s -search and capture.
675s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
675s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
675s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
675s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
675s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
675s CMD finished (0 seconds)
675s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
675s CMD finished (0 seconds)
675s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
675s CMD finished (0 seconds)
675s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
675s CMD finished (0 seconds)
675s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads
675s 
675s 
675s Normalization complete. See outputs: 
675s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
675s 	/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
675s Wednesday, October 29, 2025: 03:54:46	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok
675s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:54:46	CMD: cat /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
675s Wednesday, October 29, 2025: 03:54:46	CMD: cat /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
675s Wednesday, October 29, 2025: 03:54:46	CMD: touch left.fa.ok
675s Wednesday, October 29, 2025: 03:54:46	CMD: touch right.fa.ok
675s Wednesday, October 29, 2025: 03:54:46	CMD: touch left.fa.ok right.fa.ok
675s Wednesday, October 29, 2025: 03:54:46	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
675s Wednesday, October 29, 2025: 03:54:46	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok
675s WARNING:  --no_run_inchworm parameter in effect.  Stopping here prior to running inchworm.
675s 
675s # stop before chrysalis
675s ${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
675s 
675s 
675s      ______  ____   ____  ____   ____  ______  __ __
675s     |      ||    \ |    ||    \ |    ||      ||  |  |
675s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
675s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
675s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
675s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
675s       |__|  |__|\_||____||__|__||____|  |__|  |____/
675s 
675s     Trinity-v2.15.2
675s 
675s 
675s 
675s Left read files: $VAR1 = [
675s           'reads.left.fq.gz'
675s         ];
675s Right read files: $VAR1 = [
675s           'reads.right.fq.gz'
675s         ];
675s 
675s 
675s ----------------------------------------------------------------------------------
675s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
675s ----------------------------------------------------------------------------------
675s 
675s ---------------------------------------------------------------
675s ------------ In silico Read Normalization ---------------------
675s -- (Removing Excess Reads Beyond 200 Coverage --
675s ---------------------------------------------------------------
675s 
675s # running normalization on reads: $VAR1 = [
675s           [
675s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
675s           ],
675s           [
675s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
675s           ]
675s         ];
675s 
675s 
675s -------------------------------------------
675s ----------- Jellyfish  --------------------
675s -- (building a k-mer (25) catalog from reads) --
675s -------------------------------------------
675s 
675s * [Wed Oct 29 03:54:46 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
676s * [Wed Oct 29 03:54:46 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
676s * [Wed Oct 29 03:54:46 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
676s ----------------------------------------------
676s --------------- Inchworm (K=25, asm) ---------------------
676s -- (Linear contig construction from k-mers) --
676s ----------------------------------------------
676s 
676s * [Wed Oct 29 03:54:46 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp
676s Kmer length set to: 25
676s Min assembly length set to: 25
676s Monitor turned on, set to: 1
676s double stranded mode set
676s min entropy set to: 1
676s setting number of threads to: 2
676s -setting parallel iworm mode.
676s -reading Kmer occurrences...
676s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
676s  done parsing 517949 Kmers, 517949 added, taking 1 seconds.
676s 
676s TIMING KMER_DB_BUILDING 1 s.
676s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
676s Pruned 4114 kmers from catalog.
676s 	Pruning time: 0 seconds = 0 minutes.
676s 
676s TIMING PRUNING 0 s.
676s -populating the kmer seed candidate list.
676s Kcounter hash size: 517949
676s Processed 513835 non-zero abundance kmers in kcounter.
676s -Not sorting list of kmers, given parallel mode in effect.
676s -beginning inchworm contig assembly.
676s Total kcounter hash size: 517949 vs. sorted list size: 513835
676s num threads set to: 2
676s Done opening file. tmp.iworm.fa.pid_83449.thread_0
676s Done opening file. tmp.iworm.fa.pid_83449.thread_1
677s 
677s 	Iworm contig assembly time: 0 seconds = 0 minutes.
677s 
677s TIMING CONTIG_BUILDING 0 s.
677s 
677s TIMING PROG_RUNTIME 1 s.
677s * [Wed Oct 29 03:54:47 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa
677s Wednesday, October 29, 2025: 03:54:47	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished
677s 
677s 
677s 
677s #########################################################################
677s Inchworm is complete.  --no_run_chrysalis was specified, so stopping here.
677s #########################################################################
677s 
677s 
677s 
677s # stop before phase 2
677s ${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
677s 
677s 
677s      ______  ____   ____  ____   ____  ______  __ __
677s     |      ||    \ |    ||    \ |    ||      ||  |  |
677s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
677s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
677s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
677s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
677s       |__|  |__|\_||____||__|__||____|  |__|  |____/
677s 
677s     Trinity-v2.15.2
677s 
677s 
677s 
677s Left read files: $VAR1 = [
677s           'reads.left.fq.gz'
677s         ];
677s Right read files: $VAR1 = [
677s           'reads.right.fq.gz'
677s         ];
677s 
677s 
677s ----------------------------------------------------------------------------------
677s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
677s ----------------------------------------------------------------------------------
677s 
677s ---------------------------------------------------------------
677s ------------ In silico Read Normalization ---------------------
677s -- (Removing Excess Reads Beyond 200 Coverage --
677s ---------------------------------------------------------------
677s 
677s # running normalization on reads: $VAR1 = [
677s           [
677s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
677s           ],
677s           [
677s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
677s           ]
677s         ];
677s 
677s 
677s --------------------------------------------------------
677s -------------------- Chrysalis -------------------------
677s -- (Contig Clustering & de Bruijn Graph Construction) --
677s --------------------------------------------------------
677s 
677s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
677s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
677s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
677s 
677s 
677s #######################################################################
677s Inchworm file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
677s Skipping Inchworm Step, Using Previous Inchworm Assembly
677s #######################################################################
677s 
677s * [Wed Oct 29 03:54:47 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100
677s * [Wed Oct 29 03:54:47 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null
677s * [Wed Oct 29 03:54:47 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 
680s * [Wed Oct 29 03:54:50 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt
680s * [Wed Oct 29 03:54:50 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt
681s * [Wed Oct 29 03:54:51 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted
681s * [Wed Oct 29 03:54:51 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
681s * [Wed Oct 29 03:54:51 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out
681s * [Wed Oct 29 03:54:51 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200
681s * [Wed Oct 29 03:54:51 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
683s * [Wed Oct 29 03:54:53 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort
683s Wednesday, October 29, 2025: 03:54:53	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0
683s Wednesday, October 29, 2025: 03:54:53	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok
683s Wednesday, October 29, 2025: 03:54:53	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
683s Wednesday, October 29, 2025: 03:54:53	CMD: touch recursive_trinity.cmds.ok
683s Wednesday, October 29, 2025: 03:54:53	CMD: touch recursive_trinity.cmds.ok
683s 
683s 
683s ###################################################################
683s ##  Stopping here due to --no_distributed_trinity_exec in effect ##
683s ###################################################################
683s 
683s 
683s # finish it up
683s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal 
683s 
683s 
683s      ______  ____   ____  ____   ____  ______  __ __
683s     |      ||    \ |    ||    \ |    ||      ||  |  |
683s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
683s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
683s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
683s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
683s       |__|  |__|\_||____||__|__||____|  |__|  |____/
683s 
683s     Trinity-v2.15.2
683s 
683s 
683s 
683s Left read files: $VAR1 = [
683s           'reads.left.fq.gz'
683s         ];
683s Right read files: $VAR1 = [
683s           'reads.right.fq.gz'
683s         ];
683s 
683s 
683s ----------------------------------------------------------------------------------
683s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
683s ----------------------------------------------------------------------------------
683s 
683s ---------------------------------------------------------------
683s ------------ In silico Read Normalization ---------------------
683s -- (Removing Excess Reads Beyond 200 Coverage --
683s ---------------------------------------------------------------
683s 
683s # running normalization on reads: $VAR1 = [
683s           [
683s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
683s           ],
683s           [
683s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
683s           ]
683s         ];
683s 
683s 
683s --------------------------------------------------------
683s -------------------- Chrysalis -------------------------
683s -- (Contig Clustering & de Bruijn Graph Construction) --
683s --------------------------------------------------------
683s 
683s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
683s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
683s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
683s 
683s 
683s #######################################################################
683s Inchworm file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
683s Skipping Inchworm Step, Using Previous Inchworm Assembly
683s #######################################################################
683s 
683s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists.
683s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists.
683s -- 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists.
683s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists.
683s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists.
683s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists.
683s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists.
683s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists.
683s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists.
683s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 , checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists.
683s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists.
683s 
683s 
683s --------------------------------------------------------------------------------
683s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
683s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
683s --------------------------------------------------------------------------------
683s 
683s Wednesday, October 29, 2025: 03:54:53	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
683s Number of Commands: 38
718s 
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.    
718s 
718s All commands completed successfully. :-)
718s 
718s 
718s 
718s ** Harvesting all assembled transcripts into a single multi-fasta file...
718s 
718s Wednesday, October 29, 2025: 03:55:28	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp
718s * [Wed Oct 29 03:55:28 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2
719s * [Wed Oct 29 03:55:29 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
719s Wednesday, October 29, 2025: 03:55:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map
719s 
719s 
719s #############################################################################
719s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
719s #############################################################################
719s 
719s 
719s 
719s 
719s 
719s 
719s ##### Done Running Trinity #####
719s 
719s exit 0
719s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh
719s #!/bin/bash -ve
719s 
719s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
719s               --seqType fq \
719s               --max_memory 1G \
719s               --min_kmer_cov 3 \
719s               --output trinity_test_samples_PE_min_kmer_cov_3
719s 
719s 
719s      ______  ____   ____  ____   ____  ______  __ __
719s     |      ||    \ |    ||    \ |    ||      ||  |  |
719s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
719s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
719s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
719s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
719s       |__|  |__|\_||____||__|__||____|  |__|  |____/
719s 
719s     Trinity-v2.15.2
719s 
719s 
719s 
719s Left read files: $VAR1 = [
719s           'reads.left.fq.gz',
719s           'reads2.left.fq.gz'
719s         ];
719s Right read files: $VAR1 = [
719s           'reads.right.fq.gz',
719s           'reads2.right.fq.gz'
719s         ];
719s Wednesday, October 29, 2025: 03:55:29	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3
719s Wednesday, October 29, 2025: 03:55:29	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis
719s 
719s 
719s ----------------------------------------------------------------------------------
719s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
719s ----------------------------------------------------------------------------------
719s 
719s ---------------------------------------------------------------
719s ------------ In silico Read Normalization ---------------------
719s -- (Removing Excess Reads Beyond 200 Coverage --
719s ---------------------------------------------------------------
719s 
719s # running normalization on reads: $VAR1 = [
719s           [
719s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
719s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
719s           ],
719s           [
719s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
719s             '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
719s           ]
719s         ];
719s 
719s 
719s Wednesday, October 29, 2025: 03:55:29	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
719s -prepping seqs
719s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
719s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
719s CMD finished (0 seconds)
719s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
719s CMD finished (0 seconds)
719s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
719s CMD finished (0 seconds)
719s CMD finished (0 seconds)
719s CMD: touch left.fa.ok
719s CMD finished (0 seconds)
719s CMD: touch right.fa.ok
719s CMD finished (0 seconds)
719s  Done converting input files. CMD: cat left.fa right.fa > both.fa
719s CMD finished (0 seconds)
719s CMD: touch both.fa.ok
719s CMD finished (0 seconds)
719s -kmer counting.
719s -------------------------------------------
719s ----------- Jellyfish  --------------------
719s -- (building a k-mer catalog from reads) --
719s -------------------------------------------
719s 
719s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
720s CMD finished (1 seconds)
720s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
720s CMD finished (0 seconds)
720s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
720s CMD finished (0 seconds)
720s CMD: touch jellyfish.K25.min2.kmers.fa.success
720s CMD finished (0 seconds)
720s -generating stats files
720s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
720s -reading Kmer occurrences...
720s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
720s -reading Kmer occurrences...
720s 
720s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
720s 
720s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
721s STATS_GENERATION_TIME: 1 seconds.
721s STATS_GENERATION_TIME: 1 seconds.
721s CMD finished (1 seconds)
721s CMD finished (1 seconds)
721s CMD: touch left.fa.K25.stats.ok
721s CMD finished (0 seconds)
721s CMD: touch right.fa.K25.stats.ok
721s CMD finished (0 seconds)
721s -sorting each stats file by read name.
721s 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
721s 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
721s CMD finished (0 seconds)
721s CMD finished (0 seconds)
721s CMD: touch left.fa.K25.stats.sort.ok
721s CMD finished (0 seconds)
721s CMD: touch right.fa.K25.stats.sort.ok
721s CMD finished (0 seconds)
721s -defining normalized reads
721s 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
721s -opening left.fa.K25.stats.sort
721s -opening right.fa.K25.stats.sort
721s -done opening files.
721s CMD finished (0 seconds)
721s CMD: touch pairs.K25.stats.ok
721s CMD finished (0 seconds)
721s 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
721s 53574 / 61150 = 87.61% reads selected during normalization.
721s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
721s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3
721s CMD finished (1 seconds)
721s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
721s CMD finished (0 seconds)
721s -search and capture.
722s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
722s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
722s -preparing to extract selected reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
722s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
722s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
722s -capturing normalized reads from: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
722s CMD: touch /tmp/autopkgtest.Uv0c5G/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
722s CMD finished (0 seconds)
722s CMD: touch /tmp/autopkgtest.Uv0c5G/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
722s CMD finished (0 seconds)
722s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
722s CMD finished (0 seconds)
722s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/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
722s CMD finished (0 seconds)
722s -removing tmp dir /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads
722s 
722s 
722s Normalization complete. See outputs: 
722s 	/tmp/autopkgtest.Uv0c5G/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
722s 	/tmp/autopkgtest.Uv0c5G/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
722s Wednesday, October 29, 2025: 03:55:32	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok
722s Converting input files. (in parallel)Wednesday, October 29, 2025: 03:55:32	CMD: cat /tmp/autopkgtest.Uv0c5G/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
722s Wednesday, October 29, 2025: 03:55:32	CMD: cat /tmp/autopkgtest.Uv0c5G/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
722s Wednesday, October 29, 2025: 03:55:32	CMD: touch left.fa.ok
722s Wednesday, October 29, 2025: 03:55:32	CMD: touch right.fa.ok
722s Wednesday, October 29, 2025: 03:55:32	CMD: touch left.fa.ok right.fa.ok
722s Wednesday, October 29, 2025: 03:55:32	CMD: cat left.fa right.fa > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
722s Wednesday, October 29, 2025: 03:55:32	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok
722s -------------------------------------------
722s ----------- Jellyfish  --------------------
722s -- (building a k-mer (25) catalog from reads) --
722s -------------------------------------------
722s 
722s * [Wed Oct 29 03:55:32 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
723s * [Wed Oct 29 03:55:33 2025] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
723s * [Wed Oct 29 03:55:33 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
723s ----------------------------------------------
723s --------------- Inchworm (K=25, asm) ---------------------
723s -- (Linear contig construction from k-mers) --
723s ----------------------------------------------
723s 
723s * [Wed Oct 29 03:55:33 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp
723s Kmer length set to: 25
723s Min assembly length set to: 25
723s Monitor turned on, set to: 1
723s double stranded mode set
723s min entropy set to: 1
723s setting number of threads to: 2
723s -setting parallel iworm mode.
723s -reading Kmer occurrences...
723s 
723s  done parsing 96295 Kmers, 96295 added, taking 0 seconds.
723s 
723s TIMING KMER_DB_BUILDING 0 s.
723s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
723s Pruned 474 kmers from catalog.
723s 	Pruning time: 0 seconds = 0 minutes.
723s 
723s TIMING PRUNING 0 s.
723s -populating the kmer seed candidate list.
723s Kcounter hash size: 96295
723s Processed 95821 non-zero abundance kmers in kcounter.
723s -Not sorting list of kmers, given parallel mode in effect.
723s -beginning inchworm contig assembly.
723s Total kcounter hash size: 96295 vs. sorted list size: 95821
723s num threads set to: 2
723s Done opening file. tmp.iworm.fa.pid_90423.thread_0
723s Done opening file. tmp.iworm.fa.pid_90423.thread_1
723s 
723s 	Iworm contig assembly time: 0 seconds = 0 minutes.
723s 
723s TIMING CONTIG_BUILDING 0 s.
723s 
723s TIMING PROG_RUNTIME 0 s.
723s * [Wed Oct 29 03:55:33 2025] Running CMD: mv /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa
723s Wednesday, October 29, 2025: 03:55:33	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished
723s --------------------------------------------------------
723s -------------------- Chrysalis -------------------------
723s -- (Contig Clustering & de Bruijn Graph Construction) --
723s --------------------------------------------------------
723s 
723s inchworm_target: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
723s bowtie_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
723s chrysalis_reads_fa: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
723s * [Wed Oct 29 03:55:33 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100
723s * [Wed Oct 29 03:55:33 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null
723s * [Wed Oct 29 03:55:34 2025] 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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 
728s * [Wed Oct 29 03:55:38 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt
729s * [Wed Oct 29 03:55:39 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt
730s * [Wed Oct 29 03:55:40 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted
730s * [Wed Oct 29 03:55:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
730s * [Wed Oct 29 03:55:40 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out
730s * [Wed Oct 29 03:55:40 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200
730s * [Wed Oct 29 03:55:40 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.Uv0c5G/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 
733s * [Wed Oct 29 03:55:43 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort
733s Wednesday, October 29, 2025: 03:55:43	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0
733s Wednesday, October 29, 2025: 03:55:43	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok
733s Wednesday, October 29, 2025: 03:55:43	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.Uv0c5G/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
733s Wednesday, October 29, 2025: 03:55:43	CMD: touch recursive_trinity.cmds.ok
733s Wednesday, October 29, 2025: 03:55:43	CMD: touch recursive_trinity.cmds.ok
733s 
733s 
733s --------------------------------------------------------------------------------
733s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
733s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
733s --------------------------------------------------------------------------------
733s 
733s Wednesday, October 29, 2025: 03:55:43	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
733s Number of Commands: 17
764s 
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.    
764s 
764s All commands completed successfully. :-)
764s 
764s 
764s 
764s ** Harvesting all assembled transcripts into a single multi-fasta file...
764s 
764s Wednesday, October 29, 2025: 03:56:15	CMD: find /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp
764s * [Wed Oct 29 03:56:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2
765s * [Wed Oct 29 03:56:16 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
765s Wednesday, October 29, 2025: 03:56:16	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta.gene_trans_map
765s 
765s 
765s #############################################################################
765s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
765s #############################################################################
765s 
765s 
765s 
765s 
765s exit 0
765s touch test_all
765s make[1]: Leaving directory '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
766s Running example in test_GenomeGuidedTrinity...
766s make[1]: Entering directory '/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
766s ./run_genome-guided_Trinity_use_existing_bam.sh
766s #!/bin/bash -ve
766s 
766s if [ -e top100k.Left.fq.gz ] && ! [ -e top100k.Left.fq ]
766s then
766s 	gunzip -c top100k.Left.fq.gz > top100k.Left.fq
766s fi
766s 
766s if [ -e top100k.Right.fq.gz ] && ! [ -e top100k.Right.fq ]
766s then
766s 	gunzip -c top100k.Right.fq.gz > top100k.Right.fq
766s fi
766s 
766s 
766s 
766s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ]
766s then
766s 	gunzip -c top100k.genome.gz > top100k.genome
766s fi
766s 
766s 
766s 
766s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G  --output test_GG_use_bam_trinity_outdir
766s 
766s 
766s      ______  ____   ____  ____   ____  ______  __ __
766s     |      ||    \ |    ||    \ |    ||      ||  |  |
766s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
766s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
766s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
766s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
766s       |__|  |__|\_||____||__|__||____|  |__|  |____/
766s 
766s     Trinity-v2.15.2
766s 
766s 
766s 
766s Wednesday, October 29, 2025: 03:56:16	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
766s -appears to be a coordinate sorted bam file. ok.
766s Wednesday, October 29, 2025: 03:56:16	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir
766s 
766s 
766s ----------------------------------------------------------------------------------
766s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
766s ----------------------------------------------------------------------------------
766s 
766s -found paired-end aligned read. Running in paired-end mode.
766s Wednesday, October 29, 2025: 03:56:16	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
766s Wednesday, October 29, 2025: 03:56:17	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok
766s Wednesday, October 29, 2025: 03:56:17	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.Uv0c5G/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 
766s 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 
766s -extracting read coordinates from SP2.chr.bam.norm_200.bam into SP2.chr.bam.norm_200.bam.read_coords
766s 
767s CMD: touch SP2.chr.bam.norm_200.bam.read_coords.ok
767s 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
767s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
767s 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
767s 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
767s 
[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
767s 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
767s CMD: touch SP2.chr.bam.norm_200.bam.minC1.gff.ok
767s 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 
767s // parsing paritions.
767s 
[71]  -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14_122.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/2163_3611.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/4913_5681.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/11319_11903.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/12073_12996.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/15124_16713.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17151_17239.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17291_17395.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17403_17460.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17486_18615.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/18669_19255.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/25542_25904.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/27107_27961.trinity.reads
767s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/29764_32484.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
768s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads
768s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok
768s ##
768s Done
768s ##
768s 
768s Wednesday, October 29, 2025: 03:56:18	CMD: touch partitions.ok
768s Wednesday, October 29, 2025: 03:56:18	CMD: find Dir_* -name '*reads' > read_files.list
768s Wednesday, October 29, 2025: 03:56:18	CMD: touch read_files.list.ok
768s Wednesday, October 29, 2025: 03:56:18	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
768s Wednesday, October 29, 2025: 03:56:18	CMD: touch trinity_GG.cmds.ok
768s Wednesday, October 29, 2025: 03:56:18	CMD: touch trinity_GG.cmds.ok
768s 
768s 
768s --------------------------------------------------------------------------------
768s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
768s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
768s --------------------------------------------------------------------------------
768s 
768s Wednesday, October 29, 2025: 03:56:18	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
768s Number of Commands: 37
796s 
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.    
796s 
796s All commands completed successfully. :-)
796s 
796s Wednesday, October 29, 2025: 03:56:46	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp
796s Wednesday, October 29, 2025: 03:56:46	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
796s 
796s 
796s Finished. See /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
796s 
796s 
796s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta")
796s ok
796s if [ $asmsize -le 50000 ]; then
796s     echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete"
796s     exit 1
796s else
796s     echo "ok"
796s     exit 0
796s fi
796s ./run_Schizo_TrinityGG_jaccard_clip.sh
796s #!/bin/bash -ve
796s 
796s $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
796s 
796s 
796s      ______  ____   ____  ____   ____  ______  __ __
796s     |      ||    \ |    ||    \ |    ||      ||  |  |
796s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
796s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
796s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
796s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
796s       |__|  |__|\_||____||__|__||____|  |__|  |____/
796s 
796s     Trinity-v2.15.2
796s 
796s 
796s 
796s Wednesday, October 29, 2025: 03:56:46	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
796s -appears to be a coordinate sorted bam file. ok.
796s Wednesday, October 29, 2025: 03:56:46	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir
796s 
796s 
796s ----------------------------------------------------------------------------------
796s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
796s ----------------------------------------------------------------------------------
796s 
796s -found paired-end aligned read. Running in paired-end mode.
796s Wednesday, October 29, 2025: 03:56:46	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
796s Wednesday, October 29, 2025: 03:56:46	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok
796s Wednesday, October 29, 2025: 03:56:46	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.Uv0c5G/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 
796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF
797s 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 
797s 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 
797s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords
797s 
797s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords
797s 
797s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok
797s 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
797s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
797s 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
797s 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
797s 
[1000 lines read]  scaff:7000000090838467 lend:6194  rend:6433     
[2000 lines read]  scaff:7000000090838467 lend:46308  rend:46696     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok
797s 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
797s 
[3000 lines read]  scaff:7000000090838467 lend:59573  rend:59951     CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
797s 
[4000 lines read]  scaff:7000000090838467 lend:60068  rend:60313     
[5000 lines read]  scaff:7000000090838467 lend:60602  rend:60807     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
797s 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
797s 
[6000 lines read]  scaff:7000000090838467 lend:65099  rend:65468     
[1000 lines read]  scaff:7000000090838467 lend:8022  rend:8237     
[7000 lines read]  scaff:7000000090838467 lend:65621  rend:65957     
[2000 lines read]  scaff:7000000090838467 lend:8568  rend:8635     
[8000 lines read]  scaff:7000000090838467 lend:66173  rend:66538     
[3000 lines read]  scaff:7000000090838467 lend:21591  rend:21888     
[4000 lines read]  scaff:7000000090838467 lend:29215  rend:29340     
[9000 lines read]  scaff:7000000090838467 lend:88962  rend:89278     
[5000 lines read]  scaff:7000000090838467 lend:30519  rend:30759     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok
797s 
[6000 lines read]  scaff:7000000090838467 lend:52660  rend:52989     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
797s 
[7000 lines read]  scaff:7000000090838467 lend:56475  rend:56834     
[8000 lines read]  scaff:7000000090838467 lend:57224  rend:57489     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
797s 
[9000 lines read]  scaff:7000000090838467 lend:67627  rend:67818     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 
797s 
[10000 lines read]  scaff:7000000090838467 lend:68505  rend:68690     // parsing paritions.
797s 
[73]  -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
797s 
[11000 lines read]  scaff:7000000090838467 lend:69245  rend:69544     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads
797s 
[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
797s 
[13000 lines read]  scaff:7000000090838467 lend:83622  rend:83842     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads
797s 
[14000 lines read]  scaff:7000000090838467 lend:84137  rend:84436     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok
797s 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
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads
797s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
797s 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 
797s // parsing paritions.
797s 
[57]  -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads
797s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads
798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads
798s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
798s ##
798s Done
798s ##
798s 
798s Wednesday, October 29, 2025: 03:56:48	CMD: touch partitions.ok
798s Wednesday, October 29, 2025: 03:56:48	CMD: find Dir_* -name '*reads' > read_files.list
798s Wednesday, October 29, 2025: 03:56:48	CMD: touch read_files.list.ok
798s Wednesday, October 29, 2025: 03:56:48	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
798s Wednesday, October 29, 2025: 03:56:48	CMD: touch trinity_GG.cmds.ok
798s Wednesday, October 29, 2025: 03:56:48	CMD: touch trinity_GG.cmds.ok
798s 
798s 
798s --------------------------------------------------------------------------------
798s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
798s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
798s --------------------------------------------------------------------------------
798s 
798s Wednesday, October 29, 2025: 03:56:48	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
798s Number of Commands: 53
798s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
798s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
798s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s bt2 index files: $VAR1 = [];
798s Note - bowtie-build indices do not yet exist. Indexing genome now.
798s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s bt2 index files: $VAR1 = [];
798s Note - bowtie-build indices do not yet exist. Indexing genome now.
798s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
798s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
798s 42 reads; of these:
798s   42 (100.00%) were unpaired; of these:
798s     18 (42.86%) aligned 0 times
798s     24 (57.14%) aligned exactly 1 time
798s     0 (0.00%) aligned >1 times
798s 57.14% overall alignment rate
798s 46 reads; of these:
798s   46 (100.00%) were unpaired; of these:
798s     0 (0.00%) aligned 0 times
798s     44 (95.65%) aligned exactly 1 time
798s     2 (4.35%) aligned >1 times
798s 100.00% overall alignment rate
798s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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_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 CMD: /usr/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 
798s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
798s 
798s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
798s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
798s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
798s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
798s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
798s -processing jaccard pair sensor
798s -processing jaccard pair sensor
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s 
succeeded(1)   1.88679% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
799s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s bt2 index files: $VAR1 = [];
799s Note - bowtie-build indices do not yet exist. Indexing genome now.
799s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s 
succeeded(2)   3.77358% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
799s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
799s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s bt2 index files: $VAR1 = [];
799s Note - bowtie-build indices do not yet exist. Indexing genome now.
799s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s 5664 reads; of these:
799s   5664 (100.00%) were unpaired; of these:
799s     8 (0.14%) aligned 0 times
799s     3217 (56.80%) aligned exactly 1 time
799s     2439 (43.06%) aligned >1 times
799s 99.86% overall alignment rate
799s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
799s 16 reads; of these:
799s   16 (100.00%) were unpaired; of these:
799s     0 (0.00%) aligned 0 times
799s     14 (87.50%) aligned exactly 1 time
799s     2 (12.50%) aligned >1 times
799s 100.00% overall alignment rate
799s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
799s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
799s 
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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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 CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s -processing jaccard pair sensor
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
799s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
799s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
799s 
800s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
800s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
800s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
800s -processing jaccard pair sensor
800s 
succeeded(3)   5.66038% 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
800s 
[1000 lines read]  scaff:a1;95 lend:117  rend:350     
[2000 lines read]  scaff:a1;95 lend:928  rend:1277     CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
800s 
[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     CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s bt2 index files: $VAR1 = [];
800s Note - bowtie-build indices do not yet exist. Indexing genome now.
800s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s 
[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
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
800s 1811 reads; of these:
800s   1811 (100.00%) were unpaired; of these:
800s     6 (0.33%) aligned 0 times
800s     1189 (65.65%) aligned exactly 1 time
800s     616 (34.01%) aligned >1 times
800s 99.67% overall alignment rate
800s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
800s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
800s 
800s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
800s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
800s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
800s -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
800s 
[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
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
802s 
succeeded(4)   7.54717% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
802s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
802s bt2 index files: $VAR1 = [];
802s Note - bowtie-build indices do not yet exist. Indexing genome now.
802s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s 
succeeded(5)   9.43396% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
803s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
803s 1717 reads; of these:
803s   1717 (100.00%) were unpaired; of these:
803s     1 (0.06%) aligned 0 times
803s     1511 (88.00%) aligned exactly 1 time
803s     205 (11.94%) aligned >1 times
803s 99.94% overall alignment rate
803s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s bt2 index files: $VAR1 = [];
803s Note - bowtie-build indices do not yet exist. Indexing genome now.
803s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
803s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
803s 
803s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
803s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
803s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
803s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
803s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
803s -processing jaccard pair sensor
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
803s 997 reads; of these:
803s   997 (100.00%) were unpaired; of these:
803s     3 (0.30%) aligned 0 times
803s     568 (56.97%) aligned exactly 1 time
803s     426 (42.73%) aligned >1 times
803s 99.70% overall alignment rate
803s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s 
[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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
803s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
803s 
803s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
803s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
803s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
803s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
803s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
803s -processing jaccard pair sensor
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
803s 
[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
803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s 
succeeded(6)   11.3208% completed.    
succeeded(7)   13.2075% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
805s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s bt2 index files: $VAR1 = [];
805s Note - bowtie-build indices do not yet exist. Indexing genome now.
805s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
805s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s bt2 index files: $VAR1 = [];
805s Note - bowtie-build indices do not yet exist. Indexing genome now.
805s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
805s 85 reads; of these:
805s   85 (100.00%) were unpaired; of these:
805s     6 (7.06%) aligned 0 times
805s     79 (92.94%) aligned exactly 1 time
805s     0 (0.00%) aligned >1 times
805s 92.94% overall alignment rate
805s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
805s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
805s 
805s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
805s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
805s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
805s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
805s -processing jaccard pair sensor
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
805s 20 reads; of these:
805s   20 (100.00%) were unpaired; of these:
805s     4 (20.00%) aligned 0 times
805s     16 (80.00%) aligned exactly 1 time
805s     0 (0.00%) aligned >1 times
805s 80.00% overall alignment rate
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
805s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
805s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
805s 
805s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
805s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
805s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
805s -processing jaccard pair sensor
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s 
succeeded(8)   15.0943% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
806s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s bt2 index files: $VAR1 = [];
806s Note - bowtie-build indices do not yet exist. Indexing genome now.
806s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s 
succeeded(9)   16.9811% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
806s 371 reads; of these:
806s   371 (100.00%) were unpaired; of these:
806s     2 (0.54%) aligned 0 times
806s     296 (79.78%) aligned exactly 1 time
806s     73 (19.68%) aligned >1 times
806s 99.46% overall alignment rate
806s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
806s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s bt2 index files: $VAR1 = [];
806s Note - bowtie-build indices do not yet exist. Indexing genome now.
806s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
806s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
806s 
806s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
806s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
806s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
806s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
806s -processing jaccard pair sensor
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
806s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
806s 16 reads; of these:
806s   16 (100.00%) were unpaired; of these:
806s     10 (62.50%) aligned 0 times
806s     6 (37.50%) aligned exactly 1 time
806s     0 (0.00%) aligned >1 times
806s 37.50% overall alignment rate
807s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s 
succeeded(10)   18.8679% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
807s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s bt2 index files: $VAR1 = [];
807s Note - bowtie-build indices do not yet exist. Indexing genome now.
807s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
807s 10 reads; of these:
807s   10 (100.00%) were unpaired; of these:
807s     7 (70.00%) aligned 0 times
807s     3 (30.00%) aligned exactly 1 time
807s     0 (0.00%) aligned >1 times
807s 30.00% overall alignment rate
807s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
807s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s 
succeeded(11)   20.7547% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
808s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s bt2 index files: $VAR1 = [];
808s Note - bowtie-build indices do not yet exist. Indexing genome now.
808s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s 
succeeded(12)   22.6415% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
808s 953 reads; of these:
808s   953 (100.00%) were unpaired; of these:
808s     4 (0.42%) aligned 0 times
808s     555 (58.24%) aligned exactly 1 time
808s     394 (41.34%) aligned >1 times
808s 99.58% overall alignment rate
808s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
808s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
808s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
808s 
808s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
808s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
808s bt2 index files: $VAR1 = [];
808s Note - bowtie-build indices do not yet exist. Indexing genome now.
808s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
808s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
808s -processing jaccard pair sensor
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
808s 
[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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
808s 454 reads; of these:
808s   454 (100.00%) were unpaired; of these:
808s     1 (0.22%) aligned 0 times
808s     368 (81.06%) aligned exactly 1 time
808s     85 (18.72%) aligned >1 times
808s 99.78% overall alignment rate
808s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
808s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
808s 
808s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
808s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
808s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
808s -processing jaccard pair sensor
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s 
succeeded(13)   24.5283% completed.    
succeeded(14)   26.4151% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
810s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s bt2 index files: $VAR1 = [];
810s Note - bowtie-build indices do not yet exist. Indexing genome now.
810s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
810s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s bt2 index files: $VAR1 = [];
810s Note - bowtie-build indices do not yet exist. Indexing genome now.
810s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
810s 10 reads; of these:
810s   10 (100.00%) were unpaired; of these:
810s     3 (30.00%) aligned 0 times
810s     7 (70.00%) aligned exactly 1 time
810s     0 (0.00%) aligned >1 times
810s 70.00% overall alignment rate
810s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
810s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
810s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
810s 
810s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
810s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
810s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
810s 51 reads; of these:
810s   51 (100.00%) were unpaired; of these:
810s     4 (7.84%) aligned 0 times
810s     47 (92.16%) aligned exactly 1 time
810s     0 (0.00%) aligned >1 times
810s 92.16% overall alignment rate
810s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s -processing jaccard pair sensor
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
810s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
810s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
810s 
810s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
810s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
810s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
810s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
810s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
810s -processing jaccard pair sensor
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s 
succeeded(15)   28.3019% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
811s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s bt2 index files: $VAR1 = [];
811s Note - bowtie-build indices do not yet exist. Indexing genome now.
811s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
811s 27 reads; of these:
811s   27 (100.00%) were unpaired; of these:
811s     6 (22.22%) aligned 0 times
811s     21 (77.78%) aligned exactly 1 time
811s     0 (0.00%) aligned >1 times
811s 77.78% overall alignment rate
811s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
811s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
811s 
811s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
811s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
811s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
811s -processing jaccard pair sensor
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s 
succeeded(16)   30.1887% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
811s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s bt2 index files: $VAR1 = [];
811s Note - bowtie-build indices do not yet exist. Indexing genome now.
811s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s 
succeeded(17)   32.0755% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
811s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
812s 26 reads; of these:
812s   26 (100.00%) were unpaired; of these:
812s     6 (23.08%) aligned 0 times
812s     20 (76.92%) aligned exactly 1 time
812s     0 (0.00%) aligned >1 times
812s 76.92% overall alignment rate
812s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
812s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
812s 
812s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
812s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
812s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
812s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
812s -processing jaccard pair sensor
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
812s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s bt2 index files: $VAR1 = [];
812s Note - bowtie-build indices do not yet exist. Indexing genome now.
812s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
812s 4380 reads; of these:
812s   4380 (100.00%) were unpaired; of these:
812s     10 (0.23%) aligned 0 times
812s     2462 (56.21%) aligned exactly 1 time
812s     1908 (43.56%) aligned >1 times
812s 99.77% overall alignment rate
812s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
812s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
812s 
812s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
812s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
812s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
812s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
812s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
812s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
812s -processing jaccard pair sensor
813s 
succeeded(18)   33.9623% 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
813s 
[1000 lines read]  scaff:a1;135 lend:78  rend:364     
[2000 lines read]  scaff:a1;135 lend:614  rend:934     
[3000 lines read]  scaff:a20;2 lend:7  rend:49     
[4000 lines read]  scaff:a34;2 lend:1  rend:36     
[5000 lines read]  scaff:a5;2 lend:1  rend:43     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
813s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s bt2 index files: $VAR1 = [];
813s Note - bowtie-build indices do not yet exist. Indexing genome now.
813s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
813s 26 reads; of these:
813s   26 (100.00%) were unpaired; of these:
813s     17 (65.38%) aligned 0 times
813s     9 (34.62%) aligned exactly 1 time
813s     0 (0.00%) aligned >1 times
813s 34.62% overall alignment rate
813s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
813s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
813s 
813s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
813s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
813s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
813s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
813s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
813s -processing jaccard pair sensor
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s 
succeeded(19)   35.8491% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
814s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s bt2 index files: $VAR1 = [];
814s Note - bowtie-build indices do not yet exist. Indexing genome now.
814s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
814s 76 reads; of these:
814s   76 (100.00%) were unpaired; of these:
814s     0 (0.00%) aligned 0 times
814s     76 (100.00%) aligned exactly 1 time
814s     0 (0.00%) aligned >1 times
814s 100.00% overall alignment rate
814s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
814s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
814s 
814s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
814s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
814s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
814s -processing jaccard pair sensor
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s 
succeeded(20)   37.7359% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
815s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s bt2 index files: $VAR1 = [];
815s Note - bowtie-build indices do not yet exist. Indexing genome now.
815s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
815s 52 reads; of these:
815s   52 (100.00%) were unpaired; of these:
815s     5 (9.62%) aligned 0 times
815s     47 (90.38%) aligned exactly 1 time
815s     0 (0.00%) aligned >1 times
815s 90.38% overall alignment rate
815s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
815s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
815s 
815s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
815s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
815s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
815s -processing jaccard pair sensor
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s 
succeeded(21)   39.6226% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
815s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
815s bt2 index files: $VAR1 = [];
815s Note - bowtie-build indices do not yet exist. Indexing genome now.
815s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
816s 30 reads; of these:
816s   30 (100.00%) were unpaired; of these:
816s     0 (0.00%) aligned 0 times
816s     18 (60.00%) aligned exactly 1 time
816s     12 (40.00%) aligned >1 times
816s 100.00% overall alignment rate
816s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
816s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
816s 
816s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
816s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
816s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
816s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
816s -processing jaccard pair sensor
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s 
succeeded(22)   41.5094% completed.    
succeeded(23)   43.3962% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
816s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s bt2 index files: $VAR1 = [];
816s Note - bowtie-build indices do not yet exist. Indexing genome now.
816s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
816s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
816s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
816s bt2 index files: $VAR1 = [];
816s Note - bowtie-build indices do not yet exist. Indexing genome now.
816s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s 3962 reads; of these:
817s   3962 (100.00%) were unpaired; of these:
817s     2 (0.05%) aligned 0 times
817s     2253 (56.87%) aligned exactly 1 time
817s     1707 (43.08%) aligned >1 times
817s 99.95% overall alignment rate
817s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
817s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
817s 2557 reads; of these:
817s   2557 (100.00%) were unpaired; of these:
817s     11 (0.43%) aligned 0 times
817s     1332 (52.09%) aligned exactly 1 time
817s     1214 (47.48%) aligned >1 times
817s 99.57% overall alignment rate
817s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
817s 
817s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
817s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
817s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
817s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
817s 
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
817s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
817s -processing jaccard pair sensor
817s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
817s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
817s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
817s -processing jaccard pair sensor
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
817s 
[1000 lines read]  scaff:a21;2 lend:1  rend:35     
[2000 lines read]  scaff:a38;2 lend:1  rend:49     
[1000 lines read]  scaff:a1;81 lend:250  rend:502     
[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     
[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
817s 
[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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s 
succeeded(24)   45.283% completed.    
succeeded(25)   47.1698% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
819s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s bt2 index files: $VAR1 = [];
819s Note - bowtie-build indices do not yet exist. Indexing genome now.
819s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
819s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s bt2 index files: $VAR1 = [];
819s Note - bowtie-build indices do not yet exist. Indexing genome now.
819s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
819s 10 reads; of these:
819s   10 (100.00%) were unpaired; of these:
819s     2 (20.00%) aligned 0 times
819s     8 (80.00%) aligned exactly 1 time
819s     0 (0.00%) aligned >1 times
819s 80.00% overall alignment rate
819s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
819s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
819s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
819s 
819s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
819s 818 reads; of these:
819s   818 (100.00%) were unpaired; of these:
819s     1 (0.12%) aligned 0 times
819s     758 (92.67%) aligned exactly 1 time
819s     59 (7.21%) aligned >1 times
819s 99.88% overall alignment rate
819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
819s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
819s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
819s -processing jaccard pair sensor
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
819s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
819s 
819s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
819s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
819s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
819s -processing jaccard pair sensor
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s 
succeeded(26)   49.0566% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
820s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s bt2 index files: $VAR1 = [];
820s Note - bowtie-build indices do not yet exist. Indexing genome now.
820s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
820s 85 reads; of these:
820s   85 (100.00%) were unpaired; of these:
820s     3 (3.53%) aligned 0 times
820s     82 (96.47%) aligned exactly 1 time
820s     0 (0.00%) aligned >1 times
820s 96.47% overall alignment rate
820s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
820s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
820s 
820s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
820s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
820s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
820s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
820s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
820s -processing jaccard pair sensor
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s 
succeeded(27)   50.9434% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
821s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s bt2 index files: $VAR1 = [];
821s Note - bowtie-build indices do not yet exist. Indexing genome now.
821s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
821s 18 reads; of these:
821s   18 (100.00%) were unpaired; of these:
821s     5 (27.78%) aligned 0 times
821s     13 (72.22%) aligned exactly 1 time
821s     0 (0.00%) aligned >1 times
821s 72.22% overall alignment rate
821s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
821s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
821s 
821s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
821s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
821s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
821s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
821s -processing jaccard pair sensor
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s 
succeeded(28)   52.8302% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
821s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
821s bt2 index files: $VAR1 = [];
821s Note - bowtie-build indices do not yet exist. Indexing genome now.
821s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
822s 98 reads; of these:
822s   98 (100.00%) were unpaired; of these:
822s     0 (0.00%) aligned 0 times
822s     98 (100.00%) aligned exactly 1 time
822s     0 (0.00%) aligned >1 times
822s 100.00% overall alignment rate
822s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
822s 
succeeded(29)   54.717% completed.    -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
822s 
822s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
822s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
822s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
822s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
822s -processing jaccard pair sensor
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
822s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s bt2 index files: $VAR1 = [];
822s Note - bowtie-build indices do not yet exist. Indexing genome now.
822s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
822s 1733 reads; of these:
822s   1733 (100.00%) were unpaired; of these:
822s     0 (0.00%) aligned 0 times
822s     794 (45.82%) aligned exactly 1 time
822s     939 (54.18%) aligned >1 times
822s 100.00% overall alignment rate
822s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
822s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
822s 
822s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
822s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
822s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
822s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
822s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
822s -processing jaccard pair sensor
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
822s 
[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
822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s 
succeeded(30)   56.6038% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
823s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s bt2 index files: $VAR1 = [];
823s Note - bowtie-build indices do not yet exist. Indexing genome now.
823s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
823s 54 reads; of these:
823s   54 (100.00%) were unpaired; of these:
823s     9 (16.67%) aligned 0 times
823s     45 (83.33%) aligned exactly 1 time
823s     0 (0.00%) aligned >1 times
823s 83.33% overall alignment rate
823s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
823s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
823s 
823s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
823s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
823s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
823s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
823s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
823s -processing jaccard pair sensor
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s 
succeeded(31)   58.4906% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
824s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s bt2 index files: $VAR1 = [];
824s Note - bowtie-build indices do not yet exist. Indexing genome now.
824s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s 
succeeded(32)   60.3774% completed.    CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
824s 115 reads; of these:
824s   115 (100.00%) were unpaired; of these:
824s     6 (5.22%) aligned 0 times
824s     109 (94.78%) aligned exactly 1 time
824s     0 (0.00%) aligned >1 times
824s 94.78% overall alignment rate
824s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
824s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
824s 
824s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
824s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
824s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
824s -processing jaccard pair sensor
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
824s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
824s bt2 index files: $VAR1 = [];
824s Note - bowtie-build indices do not yet exist. Indexing genome now.
824s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
825s 7038 reads; of these:
825s   7038 (100.00%) were unpaired; of these:
825s     25 (0.36%) aligned 0 times
825s     2368 (33.65%) aligned exactly 1 time
825s     4645 (66.00%) aligned >1 times
825s 99.64% overall alignment rate
825s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
825s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
825s 
825s 
succeeded(33)   62.2641% completed.    CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
825s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
825s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
826s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
826s -processing jaccard pair sensor
826s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
826s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s bt2 index files: $VAR1 = [];
826s Note - bowtie-build indices do not yet exist. Indexing genome now.
826s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
826s 34 reads; of these:
826s   34 (100.00%) were unpaired; of these:
826s     1 (2.94%) aligned 0 times
826s     33 (97.06%) aligned exactly 1 time
826s     0 (0.00%) aligned >1 times
826s 97.06% overall alignment rate
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
826s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s 
[1000 lines read]  scaff:a16;2 lend:11  rend:42     CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
826s 
[2000 lines read]  scaff:a1;131 lend:621  rend:903     CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
826s 
[3000 lines read]  scaff:a1;131 lend:1136  rend:1543     -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
826s 
826s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
826s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
826s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
826s 
[4000 lines read]  scaff:a1;131 lend:1699  rend:1900     CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
826s 
[5000 lines read]  scaff:a25;2 lend:31  rend:73     
[6000 lines read]  scaff:a30;2 lend:1  rend:37     CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
826s 
[7000 lines read]  scaff:a3;9 lend:1  rend:43     -processing jaccard pair sensor
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
826s 
[8000 lines read]  scaff:a53;2 lend:1  rend:49     
[9000 lines read]  scaff:a5;2 lend:16  rend:60     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
826s 
[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
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s 
succeeded(34)   64.1509% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
827s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s bt2 index files: $VAR1 = [];
827s Note - bowtie-build indices do not yet exist. Indexing genome now.
827s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
827s 907 reads; of these:
827s   907 (100.00%) were unpaired; of these:
827s     2 (0.22%) aligned 0 times
827s     839 (92.50%) aligned exactly 1 time
827s     66 (7.28%) aligned >1 times
827s 99.78% overall alignment rate
827s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
827s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
827s 
827s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
827s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
827s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
827s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
827s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
827s -processing jaccard pair sensor
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s 
succeeded(35)   66.0377% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
829s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s bt2 index files: $VAR1 = [];
829s Note - bowtie-build indices do not yet exist. Indexing genome now.
829s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
829s 30 reads; of these:
829s   30 (100.00%) were unpaired; of these:
829s     9 (30.00%) aligned 0 times
829s     21 (70.00%) aligned exactly 1 time
829s     0 (0.00%) aligned >1 times
829s 70.00% overall alignment rate
829s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
829s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
829s 
829s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
829s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
829s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
829s 
succeeded(36)   67.9245% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
829s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
829s -processing jaccard pair sensor
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
829s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s bt2 index files: $VAR1 = [];
829s Note - bowtie-build indices do not yet exist. Indexing genome now.
829s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
829s 24 reads; of these:
829s   24 (100.00%) were unpaired; of these:
829s     3 (12.50%) aligned 0 times
829s     21 (87.50%) aligned exactly 1 time
829s     0 (0.00%) aligned >1 times
829s 87.50% overall alignment rate
829s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
829s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
829s 
829s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
829s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
829s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
829s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
829s -processing jaccard pair sensor
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s 
succeeded(37)   69.8113% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
829s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
829s bt2 index files: $VAR1 = [];
829s Note - bowtie-build indices do not yet exist. Indexing genome now.
829s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
830s 213 reads; of these:
830s   213 (100.00%) were unpaired; of these:
830s     1 (0.47%) aligned 0 times
830s     121 (56.81%) aligned exactly 1 time
830s     91 (42.72%) aligned >1 times
830s 99.53% overall alignment rate
830s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
830s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
830s 
830s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
830s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
830s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
830s -processing jaccard pair sensor
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s 
succeeded(38)   71.6981% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
830s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s bt2 index files: $VAR1 = [];
830s Note - bowtie-build indices do not yet exist. Indexing genome now.
830s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
830s 70 reads; of these:
830s   70 (100.00%) were unpaired; of these:
830s     10 (14.29%) aligned 0 times
830s     59 (84.29%) aligned exactly 1 time
830s     1 (1.43%) aligned >1 times
830s 85.71% overall alignment rate
830s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
830s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
830s 
830s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
830s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
830s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
830s -processing jaccard pair sensor
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s 
succeeded(39)   73.5849% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
831s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s bt2 index files: $VAR1 = [];
831s Note - bowtie-build indices do not yet exist. Indexing genome now.
831s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
831s 20 reads; of these:
831s   20 (100.00%) were unpaired; of these:
831s     12 (60.00%) aligned 0 times
831s     8 (40.00%) aligned exactly 1 time
831s     0 (0.00%) aligned >1 times
831s 40.00% overall alignment rate
831s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
831s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
831s 
831s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
831s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
831s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
831s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
831s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
831s -processing jaccard pair sensor
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
831s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s 
succeeded(40)   75.4717% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
832s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s bt2 index files: $VAR1 = [];
832s Note - bowtie-build indices do not yet exist. Indexing genome now.
832s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
832s 
succeeded(41)   77.3585% completed.    2128 reads; of these:
832s   2128 (100.00%) were unpaired; of these:
832s     6 (0.28%) aligned 0 times
832s     1722 (80.92%) aligned exactly 1 time
832s     400 (18.80%) aligned >1 times
832s 99.72% overall alignment rate
832s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
832s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
832s 
832s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
832s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
832s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
832s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
832s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
832s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s -processing jaccard pair sensor
832s bt2 index files: $VAR1 = [];
832s Note - bowtie-build indices do not yet exist. Indexing genome now.
832s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
832s 
[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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
832s 538 reads; of these:
832s   538 (100.00%) were unpaired; of these:
832s     2 (0.37%) aligned 0 times
832s     530 (98.51%) aligned exactly 1 time
832s     6 (1.12%) aligned >1 times
832s 99.63% overall alignment rate
832s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
832s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
832s 
832s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
832s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
832s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
832s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
832s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
832s -processing jaccard pair sensor
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s 
succeeded(42)   79.2453% completed.    
succeeded(43)   81.1321% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
834s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
834s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s bt2 index files: $VAR1 = [];
834s Note - bowtie-build indices do not yet exist. Indexing genome now.
834s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s bt2 index files: $VAR1 = [];
834s Note - bowtie-build indices do not yet exist. Indexing genome now.
834s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
834s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
834s 24 reads; of these:
834s   24 (100.00%) were unpaired; of these:
834s     1 (4.17%) aligned 0 times
834s     23 (95.83%) aligned exactly 1 time
834s     0 (0.00%) aligned >1 times
834s 95.83% overall alignment rate
834s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s 309 reads; of these:
834s   309 (100.00%) were unpaired; of these:
834s     3 (0.97%) aligned 0 times
834s     201 (65.05%) aligned exactly 1 time
834s     105 (33.98%) aligned >1 times
834s 99.03% overall alignment rate
834s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
834s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
834s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
835s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
835s 
835s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
835s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
835s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
835s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
835s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
835s 
835s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
835s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
835s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
835s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
835s -processing jaccard pair sensor
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
835s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
835s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
835s -processing jaccard pair sensor
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s 
succeeded(44)   83.0189% completed.    
succeeded(45)   84.9057% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
836s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s bt2 index files: $VAR1 = [];
836s Note - bowtie-build indices do not yet exist. Indexing genome now.
836s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
836s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s bt2 index files: $VAR1 = [];
836s Note - bowtie-build indices do not yet exist. Indexing genome now.
836s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
836s 26 reads; of these:
836s   26 (100.00%) were unpaired; of these:
836s     0 (0.00%) aligned 0 times
836s     26 (100.00%) aligned exactly 1 time
836s     0 (0.00%) aligned >1 times
836s 100.00% overall alignment rate
836s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
836s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
836s 
836s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
836s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
836s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
836s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
836s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s -processing jaccard pair sensor
836s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s 5953 reads; of these:
836s   5953 (100.00%) were unpaired; of these:
836s     11 (0.18%) aligned 0 times
836s     3807 (63.95%) aligned exactly 1 time
836s     2135 (35.86%) aligned >1 times
836s 99.82% overall alignment rate
836s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
836s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
837s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
837s 
837s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
837s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
837s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
837s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
837s -processing jaccard pair sensor
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
837s 
[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
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s 
succeeded(46)   86.7924% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
837s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s bt2 index files: $VAR1 = [];
837s Note - bowtie-build indices do not yet exist. Indexing genome now.
837s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
837s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
838s 18 reads; of these:
838s   18 (100.00%) were unpaired; of these:
838s     1 (5.56%) aligned 0 times
838s     17 (94.44%) aligned exactly 1 time
838s     0 (0.00%) aligned >1 times
838s 94.44% overall alignment rate
838s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
838s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
838s 
838s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
838s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
838s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
838s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
838s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
838s -processing jaccard pair sensor
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s 
succeeded(47)   88.6792% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
839s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s bt2 index files: $VAR1 = [];
839s Note - bowtie-build indices do not yet exist. Indexing genome now.
839s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
839s 293 reads; of these:
839s   293 (100.00%) were unpaired; of these:
839s     0 (0.00%) aligned 0 times
839s     293 (100.00%) aligned exactly 1 time
839s     0 (0.00%) aligned >1 times
839s 100.00% overall alignment rate
839s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
839s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
839s 
839s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
839s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
839s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
839s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
839s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
839s -processing jaccard pair sensor
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s 
succeeded(48)   90.566% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
840s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s bt2 index files: $VAR1 = [];
840s Note - bowtie-build indices do not yet exist. Indexing genome now.
840s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
840s 145 reads; of these:
840s   145 (100.00%) were unpaired; of these:
840s     1 (0.69%) aligned 0 times
840s     144 (99.31%) aligned exactly 1 time
840s     0 (0.00%) aligned >1 times
840s 99.31% overall alignment rate
840s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
840s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
840s 
840s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
840s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
840s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
840s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
840s -processing jaccard pair sensor
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s 
succeeded(49)   92.4528% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
840s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s bt2 index files: $VAR1 = [];
840s Note - bowtie-build indices do not yet exist. Indexing genome now.
840s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
840s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
841s 10 reads; of these:
841s   10 (100.00%) were unpaired; of these:
841s     5 (50.00%) aligned 0 times
841s     5 (50.00%) aligned exactly 1 time
841s     0 (0.00%) aligned >1 times
841s 50.00% overall alignment rate
841s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
841s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
841s 
841s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
841s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
841s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
841s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
841s -processing jaccard pair sensor
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s 
succeeded(50)   94.3396% completed.    
succeeded(51)   96.2264% completed.    CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
841s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s bt2 index files: $VAR1 = [];
841s Note - bowtie-build indices do not yet exist. Indexing genome now.
841s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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 
841s CMD: samtools faidx /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s bt2 index files: $VAR1 = [];
841s Note - bowtie-build indices do not yet exist. Indexing genome now.
841s CMD: bowtie2-build -q /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
841s 77 reads; of these:
841s   77 (100.00%) were unpaired; of these:
841s     2 (2.60%) aligned 0 times
841s     75 (97.40%) aligned exactly 1 time
841s     0 (0.00%) aligned >1 times
841s 97.40% overall alignment rate
841s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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" 
841s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
841s 277 reads; of these:
841s   277 (100.00%) were unpaired; of these:
841s     0 (0.00%) aligned 0 times
841s     277 (100.00%) aligned exactly 1 time
841s     0 (0.00%) aligned >1 times
841s 100.00% overall alignment rate
841s CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
841s 
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
841s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
841s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
841s CMD: samtools view -bt /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
841s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
842s CMD: samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
842s -cleaning up and removing intermediate file: /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
842s CMD: ln -sf /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
842s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
842s -processing jaccard pair sensor
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
842s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
842s 
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
842s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
842s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
842s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
842s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
842s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
842s -processing jaccard pair sensor
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
842s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/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
843s 
succeeded(52)   98.1132% completed.    
succeeded(53)   100% completed.    
843s 
843s All commands completed successfully. :-)
843s 
843s Wednesday, October 29, 2025: 03:57:33	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp
843s Wednesday, October 29, 2025: 03:57:33	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map
843s 
843s 
843s Finished. See /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts
843s 
843s 
843s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta"
843s asmsize=$(wc -c <"${outfile}")
843s if [ $asmsize -le 50000 ]; then
843s     echo "Error, ${outfile} potentially incomplete"
843s     exit 1
843s else
843s     echo "ok"
843s     exit 0
843s fi
843s ok
843s ./run_small_GG_mutliScaff_test.sh
843s #!/bin/bash -ve
843s 
843s 
843s $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
843s 
843s 
843s      ______  ____   ____  ____   ____  ______  __ __
843s     |      ||    \ |    ||    \ |    ||      ||  |  |
843s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
843s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
843s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
843s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
843s       |__|  |__|\_||____||__|__||____|  |__|  |____/
843s 
843s     Trinity-v2.15.2
843s 
843s 
843s 
843s Wednesday, October 29, 2025: 03:57:33	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam
843s -appears to be a coordinate sorted bam file. ok.
843s Wednesday, October 29, 2025: 03:57:33	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir
843s 
843s 
843s ----------------------------------------------------------------------------------
843s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
843s ----------------------------------------------------------------------------------
843s 
843s -found paired-end aligned read. Running in paired-end mode.
843s Wednesday, October 29, 2025: 03:57:33	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam
844s Done with chr TRINITY_DN0_c0_g1_i1.
844s Done with chr TRINITY_DN10_c0_g1_i1.
844s Done with chr TRINITY_DN12_c0_g1_i1.
844s Done with chr TRINITY_DN12_c0_g1_i2.
844s Done with chr TRINITY_DN14_c0_g1_i1.
844s Done with chr TRINITY_DN14_c0_g2_i1.
844s Done with chr TRINITY_DN15_c0_g1_i1.
844s Done with chr TRINITY_DN16_c0_g1_i1.
844s Done with chr TRINITY_DN16_c0_g2_i1.
844s Done with chr TRINITY_DN18_c0_g1_i1.
844s Done with chr TRINITY_DN18_c0_g1_i2.
844s Done with chr TRINITY_DN19_c0_g1_i1.
844s Done with chr TRINITY_DN20_c0_g1_i1.
844s Done with chr TRINITY_DN20_c0_g2_i1.
844s Done with chr TRINITY_DN20_c0_g1_i2.
844s Done with chr TRINITY_DN20_c0_g1_i3.
844s Done with chr TRINITY_DN20_c0_g1_i4.
844s Done with chr TRINITY_DN20_c0_g1_i5.
844s Done with chr TRINITY_DN20_c0_g1_i6.
844s Done with chr TRINITY_DN20_c0_g1_i7.
844s Done with chr TRINITY_DN21_c0_g1_i1.
844s Done with chr TRINITY_DN21_c0_g1_i2.
844s Done with chr TRINITY_DN22_c0_g1_i1.
844s Done with chr TRINITY_DN22_c0_g2_i1.
844s Done with chr TRINITY_DN22_c0_g3_i1.
844s Done with chr TRINITY_DN22_c0_g4_i1.
844s Done with chr TRINITY_DN22_c0_g3_i2.
844s Done with chr TRINITY_DN22_c0_g3_i3.
844s Done with chr TRINITY_DN22_c0_g3_i4.
844s Done with chr TRINITY_DN22_c0_g5_i1.
844s Done with chr TRINITY_DN22_c0_g6_i1.
844s Done with chr TRINITY_DN22_c0_g3_i5.
844s Done with chr TRINITY_DN22_c0_g7_i1.
844s Done with chr TRINITY_DN23_c0_g1_i1.
844s Done with chr TRINITY_DN23_c0_g2_i1.
844s Done with chr TRINITY_DN23_c0_g1_i2.
844s Done with chr TRINITY_DN23_c0_g3_i1.
844s Done with chr TRINITY_DN23_c0_g4_i1.
844s Done with chr TRINITY_DN23_c0_g5_i1.
844s Done with chr TRINITY_DN23_c0_g1_i3.
844s Done with chr TRINITY_DN23_c0_g1_i4.
844s Done with chr TRINITY_DN24_c0_g1_i1.
844s Done with chr TRINITY_DN24_c0_g2_i1.
844s Done with chr TRINITY_DN24_c0_g3_i1.
844s Done with chr TRINITY_DN24_c0_g3_i2.
844s Done with chr TRINITY_DN25_c1_g1_i1.
844s Done with chr TRINITY_DN25_c1_g1_i2.
844s Done with chr TRINITY_DN25_c1_g1_i3.
844s Done with chr TRINITY_DN25_c1_g1_i4.
844s Done with chr TRINITY_DN25_c1_g1_i5.
844s Done with chr TRINITY_DN26_c0_g1_i1.
844s Done with chr TRINITY_DN26_c0_g1_i2.
844s Done with chr TRINITY_DN26_c1_g1_i1.
844s Done with chr TRINITY_DN26_c1_g1_i2.
844s Done with chr TRINITY_DN26_c1_g1_i3.
844s Done with chr TRINITY_DN26_c1_g1_i4.
844s Done with chr TRINITY_DN26_c1_g1_i5.
844s Done with chr TRINITY_DN26_c1_g1_i6.
844s Done with chr TRINITY_DN26_c1_g2_i1.
844s Done with chr TRINITY_DN26_c1_g1_i7.
844s Done with chr TRINITY_DN26_c1_g3_i1.
844s Done with chr TRINITY_DN26_c1_g1_i8.
844s Done with chr TRINITY_DN26_c1_g1_i9.
844s Done with chr TRINITY_DN26_c1_g1_i10.
844s Done with chr TRINITY_DN26_c1_g1_i11.
844s Done with chr TRINITY_DN26_c1_g3_i2.
844s Done with chr TRINITY_DN26_c1_g1_i12.
844s Done with chr TRINITY_DN26_c1_g4_i1.
844s Done with chr TRINITY_DN26_c1_g1_i13.
844s Done with chr TRINITY_DN26_c1_g1_i14.
844s Done with chr TRINITY_DN26_c1_g1_i15.
844s Done with chr TRINITY_DN26_c1_g1_i16.
844s Done with chr TRINITY_DN26_c1_g1_i17.
844s Done with chr TRINITY_DN26_c1_g1_i18.
844s Done with chr TRINITY_DN26_c1_g3_i3.
844s Done with chr TRINITY_DN26_c1_g1_i19.
844s Done with chr TRINITY_DN26_c1_g3_i4.
844s Done with chr TRINITY_DN26_c1_g5_i1.
844s Done with chr TRINITY_DN26_c1_g1_i20.
844s Done with chr TRINITY_DN26_c1_g1_i21.
844s Done with chr TRINITY_DN26_c1_g3_i5.
844s Done with chr TRINITY_DN26_c2_g1_i1.
844s Done with chr TRINITY_DN26_c2_g1_i2.
844s Done with chr TRINITY_DN26_c2_g2_i1.
844s Done with chr TRINITY_DN26_c2_g3_i1.
844s Done with chr TRINITY_DN26_c2_g1_i3.
844s Done with chr TRINITY_DN26_c2_g1_i4.
844s Done with chr TRINITY_DN26_c2_g1_i5.
844s Done with chr TRINITY_DN27_c0_g1_i1.
844s Done with chr TRINITY_DN4_c0_g1_i1.
844s Done with chr TRINITY_DN5_c0_g1_i1.
844s Wednesday, October 29, 2025: 03:57:35	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok
844s Wednesday, October 29, 2025: 03:57:35	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.Uv0c5G/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 
844s 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 
844s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords
844s 
847s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok
847s 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
847s CMD: cp /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/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
848s 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
848s 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
850s 
[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
850s 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
850s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
850s 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 
850s // parsing paritions.
850s 
[92]  -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads
850s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads
851s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads
852s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads
853s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads
854s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads
854s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
854s ##
854s Done
854s ##
854s 
854s Wednesday, October 29, 2025: 03:57:44	CMD: touch partitions.ok
854s Wednesday, October 29, 2025: 03:57:44	CMD: find Dir_* -name '*reads' > read_files.list
854s Wednesday, October 29, 2025: 03:57:44	CMD: touch read_files.list.ok
854s Wednesday, October 29, 2025: 03:57:44	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
854s Wednesday, October 29, 2025: 03:57:44	CMD: touch trinity_GG.cmds.ok
854s Wednesday, October 29, 2025: 03:57:44	CMD: touch trinity_GG.cmds.ok
854s 
854s 
854s --------------------------------------------------------------------------------
854s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
854s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
854s --------------------------------------------------------------------------------
854s 
854s Wednesday, October 29, 2025: 03:57:44	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
854s Number of Commands: 85
974s 
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.    
974s 
974s All commands completed successfully. :-)
974s 
974s Wednesday, October 29, 2025: 03:59:44	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp
974s Wednesday, October 29, 2025: 03:59:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
974s 
974s 
974s Finished. See /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
974s 
974s 
974s 
974s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta"
974s asmsize=$(wc -c <"${outfile}")
974s if [ $asmsize -le 650000 ]; then
974s     echo "Error, ${outfile} potentially incomplete"
974s     exit 1
974s else
974s     echo "ok"
974s     exit 0
974s fi
974s ok
974s ./run_chr17_GG_wLongreads.sh
974s #!/bin/bash -ve
974s 
974s 
974s $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
974s 
974s 
974s      ______  ____   ____  ____   ____  ______  __ __
974s     |      ||    \ |    ||    \ |    ||      ||  |  |
974s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
974s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
974s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
974s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
974s       |__|  |__|\_||____||__|__||____|  |__|  |____/
974s 
974s     Trinity-v2.15.2
974s 
974s 
974s 
974s Wednesday, October 29, 2025: 03:59:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam
974s -appears to be a coordinate sorted bam file. ok.
974s Wednesday, October 29, 2025: 03:59:44	CMD: mkdir -p /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir
974s 
974s 
974s ----------------------------------------------------------------------------------
974s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
974s ----------------------------------------------------------------------------------
974s 
974s -found paired-end aligned read. Running in paired-end mode.
974s Wednesday, October 29, 2025: 03:59:44	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.Uv0c5G/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.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam
975s Done with chr chr1.
975s Wednesday, October 29, 2025: 03:59:45	CMD: touch /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok
975s * [Wed Oct 29 03:59:45 2025] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam  O=/tmp/autopkgtest.Uv0c5G/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
976s INFO	2025-10-29 03:59:46	AddOrReplaceReadGroups	
976s 
976s ********** NOTE: Picard's command line syntax is changing.
976s **********
976s ********** For more information, please see:
976s ********** 
976s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
976s **********
976s ********** The command line looks like this in the new syntax:
976s **********
976s **********    AddOrReplaceReadGroups -I /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.Uv0c5G/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
976s **********
976s 
976s 
976s 03:59:46.482 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
976s 03:59:46.484 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
976s 03:59:46.484 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
976s 03:59:46.485 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
976s 03:59:46.485 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
976s 03:59:46.485 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
976s [Wed Oct 29 03:59:46 UTC 2025] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.Uv0c5G/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
976s [Wed Oct 29 03:59:46 UTC 2025] Executing as ubuntu@autopkgtest on Linux 6.17.0-5-generic amd64; OpenJDK 64-Bit Server VM 21.0.9+10-Ubuntu-1; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.3.0
976s 03:59:46.496 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
976s 03:59:46.498 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
976s INFO	2025-10-29 03:59:46	AddOrReplaceReadGroups	Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio
976s 
976s 03:59:46.528 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
976s [Wed Oct 29 03:59:46 UTC 2025] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes.
976s Runtime.totalMemory()=67108864
976s * [Wed Oct 29 03:59:46 2025] Running CMD: samtools merge /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam
977s Wednesday, October 29, 2025: 03:59:47	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.Uv0c5G/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 
977s 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 
977s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords
977s 
978s CMD: touch merged_wRGLR.bam.read_coords.ok
978s 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
978s CMD: cp /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.Uv0c5G/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname
978s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted
978s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig
990s 
[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
990s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff
992s CMD: touch merged_wRGLR.bam.minC1.gff.ok
992s 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 
992s // parsing paritions.
992s 
[100]  
[116]  -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/732418_752287.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/752375_752769.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/753167_754706.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/758974_782331.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/782362_792510.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/793543_794109.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/795176_795754.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/799707_800316.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/800915_803792.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/981902_982655.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/997125_1091796.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1146722_1146846.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1148302_1149226.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1151011_1152011.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1153293_1153810.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1226770_1227467.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1257967_1400270.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1414443_1415081.trinity.reads
992s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1420724_2022954.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2030147_2043980.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2044654_2045225.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2047917_2048512.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2049091_2049553.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2051694_2052378.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2053479_2053635.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054237_2054372.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054544_2056751.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2056812_2057391.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2058177_2058912.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2059847_2303836.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2303955_2336468.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3706252_3917856.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3923874_3964467.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3964821_3965192.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4001444_4001952.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4003050_4003706.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4004424_4555389.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4660854_4661151.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4667839_4668289.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4671192_4704136.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4704234_4705420.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4710502_4721496.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4731419_4733592.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4734646_4739376.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4787354_4789638.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4796155_4798495.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4805950_4806545.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4807192_4823373.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4833366_4897982.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4904417_4904897.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4927248_4928577.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4928729_4928949.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4929025_4934979.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935086_4935300.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935439_4945214.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4945652_4997520.trinity.reads
993s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4997681_5001302.trinity.reads
993s CMD: touch Dir_merged_wRGLR.bam.minC1.gff.ok
993s ##
993s Done
993s ##
993s 
993s Wednesday, October 29, 2025: 04:00:03	CMD: touch partitions.ok
993s Wednesday, October 29, 2025: 04:00:03	CMD: find Dir_* -name '*reads' > read_files.list
993s Wednesday, October 29, 2025: 04:00:03	CMD: touch read_files.list.ok
993s Wednesday, October 29, 2025: 04:00:03	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
993s Wednesday, October 29, 2025: 04:00:03	CMD: touch trinity_GG.cmds.ok
993s Wednesday, October 29, 2025: 04:00:03	CMD: touch trinity_GG.cmds.ok
993s 
993s 
993s --------------------------------------------------------------------------------
993s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
993s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
993s --------------------------------------------------------------------------------
993s 
993s Wednesday, October 29, 2025: 04:00:04	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 
993s Number of Commands: 44
10151s 
succeeded(1)   2.27273% completed.    
succeeded(2)   4.54545% completed.    
succeeded(3)   6.81818% completed.    
succeeded(4)   9.09091% completed.    
succeeded(5)   11.3636% completed.    
succeeded(6)   13.6364% completed.    
succeeded(7)   15.9091% completed.    
succeeded(8)   18.1818% completed.    
succeeded(9)   20.4545% completed.    
succeeded(10)   22.7273% completed.    
succeeded(11)   25% completed.    
succeeded(12)   27.2727% completed.    
succeeded(13)   29.5455% completed.    
succeeded(14)   31.8182% completed.    
succeeded(15)   34.0909% completed.    
succeeded(16)   36.3636% completed.    
succeeded(17)   38.6364% completed.    
succeeded(18)   40.9091% completed.    
succeeded(19)   43.1818% completed.    
succeeded(20)   45.4545% completed.    
succeeded(21)   47.7273% completed.    
succeeded(22)   50% completed.    
succeeded(23)   52.2727% completed.    
succeeded(24)   54.5455% completed.    
succeeded(25)   56.8182% completed.    
succeeded(26)   59.0909% completed.    
succeeded(27)   61.3636% completed.    
succeeded(28)   63.6364% completed.    
succeeded(29)   65.9091% completed.    
succeeded(30)   68.1818% completed.    
succeeded(31)   70.4545% completed.    
succeeded(32)   72.7273% completed.    
succeeded(33)   75% completed.    
succeeded(34)   77.2727% completed.    
succeeded(35)   79.5455% completed.    autopkgtest [06:32:42]: ERROR: timed out on command "su -s /bin/bash ubuntu -c set -e; exec /tmp/autopkgtest.Uv0c5G/wrapper.sh --artifacts=/tmp/autopkgtest.Uv0c5G/run-tests-artifacts --chdir=/tmp/autopkgtest.Uv0c5G/build.YC3/src --env=AUTOPKGTEST_TESTBED_ARCH=amd64 --env=AUTOPKGTEST_TEST_ARCH=amd64 --env=DEB_BUILD_OPTIONS=parallel=2 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest.Uv0c5G/run-tests-stderr --stdout=/tmp/autopkgtest.Uv0c5G/run-tests-stdout --tmp=/tmp/autopkgtest.Uv0c5G/autopkgtest_tmp --env=ADT_TEST_TRIGGERS=liburi-perl/5.34-2 --make-executable=/tmp/autopkgtest.Uv0c5G/build.YC3/src/debian/tests/run-tests -- /tmp/autopkgtest.Uv0c5G/build.YC3/src/debian/tests/run-tests" (kind: test)
10151s autopkgtest [06:32:42]: test run-tests: -----------------------]
10604s autopkgtest [06:40:15]: test run-tests:  - - - - - - - - - - results - - - - - - - - - -
10604s run-tests            FAIL timed out
10606s autopkgtest [06:40:17]: @@@@@@@@@@@@@@@@@@@@ summary
10606s run-tests            FAIL timed out