Diff of the two buildlogs: -- --- b1/build.log 2025-08-24 11:14:39.506913505 +0000 +++ b2/build.log 2025-08-24 11:23:16.495536171 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 26 05:26:35 -12 2026 -I: pbuilder-time-stamp: 1790443595 +I: Current time: Mon Aug 25 01:14:41 +14 2025 +I: pbuilder-time-stamp: 1756034081 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1907934/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 24 11:14 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fa72402514d948799bf3a2b76489db48' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1907934' - PS1='# ' - PS2='> ' + INVOCATION_ID=eeb8863937f64cb0aa18ee0af8c74129 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2326348 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S3eGOAkf/pbuilderrc_Ib8S --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S3eGOAkf/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S3eGOAkf/pbuilderrc_aVHF --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S3eGOAkf/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1907934/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -84,7 +116,7 @@ Depends: debhelper-compat (= 13), liburi-perl, ncbi-blast+, hmmer, r-base-core, r-cran-ggplot2, r-bioc-seqlogo dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19855 files and directories currently installed.) +(Reading database ... 19889 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -286,10 +318,10 @@ Get: 165 http://deb.debian.org/debian forky/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 166 http://deb.debian.org/debian forky/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 167 http://deb.debian.org/debian forky/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 133 MB in 5s (26.0 MB/s) +Fetched 133 MB in 2s (63.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19855 files and directories currently installed.) +(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 ... 19889 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. @@ -302,7 +334,7 @@ Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.6-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20189 files and directories currently installed.) +(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 ... 20223 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. @@ -338,7 +370,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. -(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 ... 21204 files and directories currently installed.) +(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 ... 21238 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package libproc2-0:amd64. @@ -846,8 +878,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Sep 26 17:29:06 UTC 2026. -Universal Time is now: Sat Sep 26 17:29:06 UTC 2026. +Local time is now: Sun Aug 24 11:16:50 UTC 2025. +Universal Time is now: Sun Aug 24 11:16:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-15) ... @@ -999,7 +1031,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes dpkg-buildpackage: info: source package transdecoder dpkg-buildpackage: info: source version 5.7.1-2 dpkg-buildpackage: info: source distribution unstable @@ -1021,7 +1057,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j16 test + make -j12 test make[2]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' @@ -1062,7 +1098,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Sat Sep 26 05:29:41 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Mon Aug 25 01:17:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -1114,13 +1150,13 @@ fi -Building a new DB, current time: 09/26/2026 05:29:42 +Building a new DB, current time: 08/25/2025 01:17:19 New DB name: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/mini_sprot.db.pep New DB title: mini_sprot.db.pep Sequence type: Protein Keep MBits: T Maximum file size: 3000000000B -Adding sequences from FASTA; added 240 sequences in 0.0571952 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00399613 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1195,8 +1231,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1765.48 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1942.31 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1254,7 +1290,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1720.22 +# Mc/sec: 2056.89 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1319,7 +1355,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2321.12 +# Mc/sec: 2661.39 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1379,8 +1415,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2476.94 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2771.42 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1440,8 +1476,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 831.34 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1081.03 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1491,8 +1527,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 680.23 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 893.24 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1557,7 +1593,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2201.73 +# Mc/sec: 2810.66 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1609,8 +1645,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 753.07 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 973.79 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1660,8 +1696,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.03 -# Mc/sec: 68.05 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2391.02 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1718,7 +1754,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2117.07 +# Mc/sec: 2741.68 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1806,8 +1842,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1822.74 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2303.05 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1891,8 +1927,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2001.67 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2654.24 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1948,8 +1984,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 1118.29 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1369.16 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -2005,8 +2041,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1073.36 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1544.87 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2063,7 +2099,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3290.94 +# Mc/sec: 3713.91 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2108,7 +2144,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2721.80 +# Mc/sec: 3165.37 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2161,7 +2197,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3514.33 +# Mc/sec: 3619.45 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2206,7 +2242,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2395.75 +# Mc/sec: 2182.32 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2267,7 +2303,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1736.94 +# Mc/sec: 2043.11 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2317,8 +2353,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.05 -# Mc/sec: 42.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1675.53 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2431,7 +2467,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1305.42 +# Mc/sec: 1511.80 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2477,8 +2513,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2280.92 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2669.56 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2544,8 +2580,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2301.86 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2640.58 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2584,7 +2620,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 4145.00 +# Mc/sec: 4289.63 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2660,8 +2696,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1623.76 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1889.78 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2714,7 +2750,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2829.88 +# Mc/sec: 3350.24 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2799,7 +2835,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 588.28 +# Mc/sec: 767.67 // Query: DLH [M=217] Accession: PF01738.17 @@ -2847,7 +2883,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3446.92 +# Mc/sec: 4516.98 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2894,7 +2930,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2296.28 +# Mc/sec: 2587.01 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2943,8 +2979,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3169.68 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3695.62 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2987,7 +3023,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3908.08 +# Mc/sec: 4300.08 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3033,7 +3069,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1388.60 +# Mc/sec: 1713.08 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3070,8 +3106,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3086.82 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3882.35 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3122,8 +3158,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1626.80 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1931.86 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3160,8 +3196,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1895.30 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2128.41 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3199,7 +3235,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3462.98 +# Mc/sec: 3470.53 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3250,7 +3286,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2097.06 +# Mc/sec: 3137.46 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3288,7 +3324,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 4250.19 +# Mc/sec: 5262.52 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3349,7 +3385,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2403.78 +# Mc/sec: 3111.53 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3394,7 +3430,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2350.37 +# Mc/sec: 3090.21 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3450,8 +3486,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2555.33 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3284.49 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3505,8 +3541,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 911.64 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1257.36 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3544,7 +3580,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 4039.87 +# Mc/sec: 4640.80 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3620,8 +3656,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2617.18 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3187.05 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3685,8 +3721,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 778.17 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1131.38 // Query: FPP [M=866] Accession: PF05911.10 @@ -3736,8 +3772,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2469.50 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2963.01 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3789,8 +3825,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.09 -# Mc/sec: 27.85 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2985.92 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3913,8 +3949,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 747.37 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 849.12 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3953,7 +3989,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1643.29 +# Mc/sec: 2036.77 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4043,8 +4079,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 857.11 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1141.22 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4094,8 +4130,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 614.47 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 799.57 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4156,7 +4192,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1697.04 +# Mc/sec: 1848.79 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4260,8 +4296,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 936.74 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1121.19 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4309,7 +4345,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2482.16 +# Mc/sec: 2846.89 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4383,8 +4419,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1575.15 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1928.63 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4454,8 +4490,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2422.49 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2429.87 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4502,8 +4538,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1090.97 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1529.45 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4574,7 +4610,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 410.94 +# Mc/sec: 543.18 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4625,7 +4661,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3350.29 +# Mc/sec: 4110.29 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4676,7 +4712,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3803.80 +# Mc/sec: 4535.15 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4715,7 +4751,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2102.12 +# Mc/sec: 2743.66 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4760,7 +4796,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2541.73 +# Mc/sec: 2599.53 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4812,7 +4848,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1865.76 +# Mc/sec: 1923.59 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4895,7 +4931,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1360.25 +# Mc/sec: 1477.41 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4995,8 +5031,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 -# Mc/sec: 984.45 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1163.45 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5051,7 +5087,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1772.98 +# Mc/sec: 2155.82 // Query: IBR [M=62] Accession: PF01485.20 @@ -5089,7 +5125,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2325.05 +# Mc/sec: 2489.40 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5136,8 +5172,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1437.86 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1813.22 // Query: malic [M=182] Accession: PF00390.18 @@ -5175,8 +5211,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 4905.09 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 5243.85 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5213,8 +5249,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1595.56 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1997.84 // Query: MatE [M=161] Accession: PF01554.17 @@ -5298,8 +5334,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.04 -# Mc/sec: 106.87 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2204.29 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5336,8 +5372,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3652.17 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4624.73 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5511,8 +5547,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 -# Mc/sec: 261.38 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 361.21 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5555,7 +5591,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2249.27 +# Mc/sec: 3006.05 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5612,7 +5648,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1140.42 +# Mc/sec: 1855.89 // Query: MIP [M=227] Accession: PF00230.19 @@ -5663,7 +5699,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2427.47 +# Mc/sec: 3646.18 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5716,7 +5752,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1425.67 +# Mc/sec: 2044.27 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5807,7 +5843,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2531.85 +# Mc/sec: 2771.62 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5845,7 +5881,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1807.60 +# Mc/sec: 2607.55 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5883,7 +5919,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3115.34 +# Mc/sec: 3649.84 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5936,7 +5972,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2360.50 +# Mc/sec: 3558.83 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5974,7 +6010,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3695.78 +# Mc/sec: 4589.82 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6095,7 +6131,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1279.76 +# Mc/sec: 1313.48 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6145,8 +6181,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3335.04 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2659.30 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6216,8 +6252,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2658.66 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3291.66 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6269,8 +6305,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08 -# Mc/sec: 131.09 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1242.11 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6332,8 +6368,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1682.29 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2040.06 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6435,8 +6471,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 361.50 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 475.59 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6484,7 +6520,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2472.65 +# Mc/sec: 2770.79 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6535,7 +6571,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1450.58 +# Mc/sec: 2023.70 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6585,8 +6621,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2290.33 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2541.30 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6636,8 +6672,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3371.87 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3556.48 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6682,7 +6718,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3361.98 +# Mc/sec: 3267.01 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6729,7 +6765,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1470.13 +# Mc/sec: 1556.69 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6794,7 +6830,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 704.07 +# Mc/sec: 943.86 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6839,7 +6875,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1866.22 +# Mc/sec: 2313.11 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6891,8 +6927,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 983.42 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1515.73 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6937,7 +6973,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3320.46 +# Mc/sec: 3321.66 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7038,7 +7074,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 728.35 +# Mc/sec: 778.82 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7082,8 +7118,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 954.04 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1167.92 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7136,7 +7172,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2755.54 +# Mc/sec: 3559.89 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7209,8 +7245,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 545.20 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 703.53 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7271,7 +7307,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2340.42 +# Mc/sec: 3293.04 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7316,7 +7352,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2622.61 +# Mc/sec: 3411.72 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7368,8 +7404,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2683.31 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2995.75 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7407,7 +7443,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 5881.59 +# Mc/sec: 7243.87 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7449,8 +7485,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2939.19 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3851.40 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7512,8 +7548,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 919.18 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1239.61 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7550,8 +7586,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3009.50 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 4386.21 // Query: Usher [M=551] Accession: PF00577.19 @@ -7595,8 +7631,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3113.32 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3818.07 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7643,7 +7679,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 808.55 +# Mc/sec: 1040.94 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7688,7 +7724,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 757.88 +# Mc/sec: 1316.36 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7733,7 +7769,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 938.15 +# Mc/sec: 1193.33 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7788,7 +7824,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1146.66 +# Mc/sec: 1485.92 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7827,7 +7863,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 790.53 +# Mc/sec: 1000.96 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7879,7 +7915,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 905.03 +# Mc/sec: 1301.41 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7926,8 +7962,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1386.71 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1952.84 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7966,14 +8002,14 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1349.78 +# Mc/sec: 1745.93 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Sat Sep 26 05:29:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Sat Sep 26 05:29:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Mon Aug 25 01:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Mon Aug 25 01:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: CUFF.60.1.p1, not unique enough -skipping training candidate: CUFF.26.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p3, not unique enough @@ -8000,39 +8036,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Sat Sep 26 05:29:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Mon Aug 25 01:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 37 -* [Sat Sep 26 05:29:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Sat Sep 26 05:29:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat Sep 26 05:29:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Mon Aug 25 01:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Mon Aug 25 01:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Mon Aug 25 01:17:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Sat Sep 26 05:29:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sat Sep 26 05:29:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sat Sep 26 05:29:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Mon Aug 25 01:17:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Mon Aug 25 01:17:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Mon Aug 25 01:17:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:30:15 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:17:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat Sep 26 05:30:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Mon Aug 25 01:17:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:30:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:17:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat Sep 26 05:30:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Mon Aug 25 01:17:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:30:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Mon Aug 25 01:17:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:30:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Mon Aug 25 01:17:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 -feature swap of score: 1.94858034627835 instead of -0.884029553505083 @@ -8042,33 +8078,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Sat Sep 26 05:30:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Mon Aug 25 01:17:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:30:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:17:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat Sep 26 05:30:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Mon Aug 25 01:17:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:30:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:17:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat Sep 26 05:30:50 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Mon Aug 25 01:17:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:30:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Mon Aug 25 01:17:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 1 -* [Sat Sep 26 05:30:51 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Sat Sep 26 05:30:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed +* [Mon Aug 25 01:17:56 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Mon Aug 25 01:17:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Sat Sep 26 05:30:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep +* [Mon Aug 25 01:17:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Sat Sep 26 05:30:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds +* [Mon Aug 25 01:17:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* @@ -8160,7 +8196,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Sat Sep 26 05:30:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat +* [Mon Aug 25 01:17:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -8184,8 +8220,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Sat Sep 26 05:30:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Sat Sep 26 05:30:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Mon Aug 25 01:17:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Mon Aug 25 01:17:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough @@ -8860,37 +8896,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Sat Sep 26 05:30:55 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Mon Aug 25 01:17:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 -* [Sat Sep 26 05:30:55 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores -* [Sat Sep 26 05:30:56 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat Sep 26 05:31:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Mon Aug 25 01:17:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores +* [Mon Aug 25 01:18:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Mon Aug 25 01:18:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat Sep 26 05:31:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sat Sep 26 05:31:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sat Sep 26 05:31:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores +* [Mon Aug 25 01:18:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Mon Aug 25 01:18:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Mon Aug 25 01:18:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:31:27 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:18:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat Sep 26 05:31:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Mon Aug 25 01:18:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:31:33 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:18:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat Sep 26 05:31:34 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Mon Aug 25 01:18:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:31:35 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Mon Aug 25 01:18:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:31:35 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced +* [Mon Aug 25 01:18:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 @@ -8949,33 +8985,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Sat Sep 26 05:31:36 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Mon Aug 25 01:18:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:31:57 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:18:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat Sep 26 05:32:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Mon Aug 25 01:18:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:32:03 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:18:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat Sep 26 05:32:04 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Mon Aug 25 01:19:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:32:05 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Mon Aug 25 01:19:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 83 -* [Sat Sep 26 05:32:05 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Sat Sep 26 05:32:05 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed +* [Mon Aug 25 01:19:01 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Mon Aug 25 01:19:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Sat Sep 26 05:32:05 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep +* [Mon Aug 25 01:19:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Sat Sep 26 05:32:06 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds +* [Mon Aug 25 01:19:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* @@ -9068,7 +9104,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Sat Sep 26 05:32:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat +* [Mon Aug 25 01:19:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -9088,8 +9124,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Sat Sep 26 05:32:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Sat Sep 26 05:32:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Mon Aug 25 01:19:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Mon Aug 25 01:19:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0_seq2.p1, not unique enough -skipping training candidate: comp992_c0_seq2.p1, not unique enough -skipping training candidate: comp718_c0_seq2.p1, not unique enough @@ -9127,37 +9163,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Sat Sep 26 05:32:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Mon Aug 25 01:19:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 -* [Sat Sep 26 05:32:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores -* [Sat Sep 26 05:32:12 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat Sep 26 05:32:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Mon Aug 25 01:19:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores +* [Mon Aug 25 01:19:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Mon Aug 25 01:19:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat Sep 26 05:32:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sat Sep 26 05:32:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sat Sep 26 05:32:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores +* [Mon Aug 25 01:19:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Mon Aug 25 01:19:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Mon Aug 25 01:19:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:32:40 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:19:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat Sep 26 05:32:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Mon Aug 25 01:19:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:32:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:19:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat Sep 26 05:32:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Mon Aug 25 01:19:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:32:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Mon Aug 25 01:19:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:32:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced +* [Mon Aug 25 01:19:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 @@ -9263,33 +9299,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Sat Sep 26 05:32:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Mon Aug 25 01:19:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:33:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:19:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat Sep 26 05:33:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Mon Aug 25 01:20:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:33:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:20:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat Sep 26 05:33:24 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Mon Aug 25 01:20:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:33:24 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Mon Aug 25 01:20:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 43 -* [Sat Sep 26 05:33:25 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Sat Sep 26 05:33:25 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed +* [Mon Aug 25 01:20:02 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Mon Aug 25 01:20:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Sat Sep 26 05:33:25 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep +* [Mon Aug 25 01:20:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Sat Sep 26 05:33:25 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds +* [Mon Aug 25 01:20:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* @@ -9306,32 +9342,32 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp1051_c1_seq1', - 'contig' => 'III', - 'orient' => '-', + 'gene_id' => '', 'trans_id' => '', + 'orient' => '-', + 'contig' => 'III', + 'asmbl' => 'comp1051_c1_seq1', 'coords' => [ [ '1642973', '1644586' ] - ], - 'gene_id' => '' + ] }; - mid_pt: 808 - strand: + + is_3prime_partial: 0 + gene_length: 1616 Model_feat_name: comp1051_c1_seq1.p1 - source: transdecoder + gene_type: protein-coding + is_5prime_partial: 0 is_pseudogene: 0 + source: transdecoder asmbl_id: comp1051_c1_seq1 num_exons: 1 - is_3prime_partial: 0 - gene_length: 1616 - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 classification: annotated_genes + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + mid_pt: 808 com_name: ORF type:5prime_partial (+),score=83.26 - is_5prime_partial: 0 - gene_type: protein-coding + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9348,10 +9384,9 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'I', - 'orient' => '-', 'gene_id' => '', 'trans_id' => '', + 'asmbl' => 'comp1058_c0_seq1', 'coords' => [ [ 5095548, @@ -9362,22 +9397,23 @@ '5095301' ] ], - 'asmbl' => 'comp1058_c0_seq1' + 'orient' => '-', + 'contig' => 'I' }; - gene_type: protein-coding - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=32.57 + is_pseudogene: 0 + asmbl_id: comp1058_c0_seq1 + num_exons: 1 + source: transdecoder classification: annotated_genes TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - gene_length: 496 + mid_pt: 248 + com_name: ORF type:5prime_partial (+),score=32.57 + strand: + is_3prime_partial: 0 - num_exons: 1 - asmbl_id: comp1058_c0_seq1 - is_pseudogene: 0 - source: transdecoder Model_feat_name: comp1058_c0_seq1.p1 - strand: + - mid_pt: 248 + gene_length: 496 + is_5prime_partial: 0 + gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9401,9 +9437,6 @@ Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'asmbl' => 'comp1112_c0_seq1', - 'orient' => '-', - 'contig' => 'III', - 'gene_id' => '', 'coords' => [ [ 2380416, @@ -9414,22 +9447,25 @@ '2380336' ] ], + 'orient' => '-', + 'contig' => 'III', + 'gene_id' => '', 'trans_id' => '' }; - num_exons: 1 gene_length: 2081 - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=155.28 - classification: annotated_genes + Model_feat_name: comp1112_c0_seq1.p1 gene_type: protein-coding is_5prime_partial: 0 - mid_pt: 1041 + is_3prime_partial: 0 strand: + - Model_feat_name: comp1112_c0_seq1.p1 + com_name: ORF type:complete (+),score=155.28 source: transdecoder + num_exons: 1 asmbl_id: comp1112_c0_seq1 is_pseudogene: 0 + mid_pt: 1041 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9452,6 +9488,10 @@ Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', + 'trans_id' => '', + 'orient' => '-', + 'contig' => 'II', + 'asmbl' => 'comp1198_c0_seq1', 'coords' => [ [ 402195, @@ -9469,26 +9509,22 @@ 401352, '401683' ] - ], - 'trans_id' => '', - 'orient' => '-', - 'contig' => 'II', - 'asmbl' => 'comp1198_c0_seq1' + ] }; - gene_type: protein-coding - is_5prime_partial: 0 - com_name: ORF type:internal (+),score=37.56 - classification: annotated_genes - is_3prime_partial: 0 - gene_length: 597 + mid_pt: 299 TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - num_exons: 1 - is_pseudogene: 0 + classification: annotated_genes asmbl_id: comp1198_c0_seq1 + num_exons: 1 source: transdecoder - Model_feat_name: comp1198_c0_seq1.p1 - mid_pt: 299 + is_pseudogene: 0 strand: + + com_name: ORF type:internal (+),score=37.56 + is_3prime_partial: 0 + is_5prime_partial: 0 + gene_type: protein-coding + Model_feat_name: comp1198_c0_seq1.p1 + gene_length: 597 gene_synonyms: mRNA_coords CDS_coords @@ -9516,10 +9552,9 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', - 'orient' => '-', 'gene_id' => '', 'trans_id' => '', + 'asmbl' => 'comp1210_c0_seq1', 'coords' => [ [ 368840, @@ -9530,22 +9565,23 @@ '368790' ] ], - 'asmbl' => 'comp1210_c0_seq1' + 'orient' => '-', + 'contig' => 'III' }; - com_name: ORF type:5prime_partial (+),score=12.16 - classification: annotated_genes - is_5prime_partial: 0 - gene_type: protein-coding - num_exons: 1 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 gene_length: 1554 + Model_feat_name: comp1210_c0_seq1.p1 + gene_type: protein-coding + is_5prime_partial: 0 is_3prime_partial: 0 + strand: + + com_name: ORF type:5prime_partial (+),score=12.16 source: transdecoder asmbl_id: comp1210_c0_seq1 + num_exons: 1 is_pseudogene: 0 - strand: + mid_pt: 777 - Model_feat_name: comp1210_c0_seq1.p1 + classification: annotated_genes + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9570,32 +9606,32 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', - 'orient' => '-', - 'trans_id' => '', + 'asmbl' => 'comp366_c0_seq1', 'coords' => [ [ '3840968', '3841303' ] ], + 'orient' => '-', + 'contig' => 'II', 'gene_id' => '', - 'asmbl' => 'comp366_c0_seq1' + 'trans_id' => '' }; + is_3prime_partial: 0 + gene_length: 340 Model_feat_name: comp366_c0_seq1.p1 - strand: - - mid_pt: 170 + gene_type: protein-coding + is_5prime_partial: 0 + source: transdecoder asmbl_id: comp366_c0_seq1 + num_exons: 1 is_pseudogene: 0 - source: transdecoder + mid_pt: 170 + classification: annotated_genes TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - gene_length: 340 - is_3prime_partial: 0 - num_exons: 1 - gene_type: protein-coding - is_5prime_partial: 0 + strand: - com_name: ORF type:internal (-),score=12.83 - classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9621,32 +9657,32 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'trans_id' => '', 'asmbl' => 'comp610_c0_seq1', - 'orient' => '-', - 'contig' => 'I', 'coords' => [ [ '5471264', '5472770' ] ], - 'trans_id' => '', - 'gene_id' => '' + 'orient' => '-', + 'contig' => 'I' }; - gene_type: protein-coding - is_5prime_partial: 0 - classification: annotated_genes com_name: ORF type:5prime_partial (+),score=50.55 - is_3prime_partial: 0 + strand: + + classification: annotated_genes TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - gene_length: 1509 - num_exons: 1 + mid_pt: 755 is_pseudogene: 0 - asmbl_id: comp610_c0_seq1 source: transdecoder + num_exons: 1 + asmbl_id: comp610_c0_seq1 + gene_type: protein-coding + is_5prime_partial: 0 + gene_length: 1509 Model_feat_name: comp610_c0_seq1.p1 - strand: + - mid_pt: 755 + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9665,32 +9701,32 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp645_c0_seq1', 'gene_id' => '', 'trans_id' => '', + 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp645_c0_seq1', 'coords' => [ [ '4333088', '4336727' ] - ], - 'orient' => '-', - 'contig' => 'I' + ] }; - num_exons: 1 + gene_type: protein-coding + is_5prime_partial: 0 gene_length: 3653 - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + Model_feat_name: comp645_c0_seq1.p1 is_3prime_partial: 0 com_name: ORF type:5prime_partial (+),score=273.35 + strand: + + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 classification: annotated_genes - gene_type: protein-coding - is_5prime_partial: 0 mid_pt: 1827 - strand: + - Model_feat_name: comp645_c0_seq1.p1 + is_pseudogene: 0 source: transdecoder + num_exons: 1 asmbl_id: comp645_c0_seq1 - is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9706,11 +9742,11 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp688_c0_seq1', - 'orient' => '+', - 'contig' => 'II', 'gene_id' => '', 'trans_id' => '', + 'orient' => '+', + 'contig' => 'II', + 'asmbl' => 'comp688_c0_seq1', 'coords' => [ [ 380308, @@ -9722,19 +9758,19 @@ ] ] }; - source: transdecoder - asmbl_id: comp688_c0_seq1 - is_pseudogene: 0 - strand: + - mid_pt: 1392 - Model_feat_name: comp688_c0_seq1.p1 com_name: ORF type:complete (+),score=172.54 + strand: + classification: annotated_genes - is_5prime_partial: 0 - gene_type: protein-coding - num_exons: 1 TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + mid_pt: 1392 + is_pseudogene: 0 + source: transdecoder + asmbl_id: comp688_c0_seq1 + num_exons: 1 + gene_type: protein-coding + is_5prime_partial: 0 gene_length: 2784 + Model_feat_name: comp688_c0_seq1.p1 is_3prime_partial: 0 gene_synonyms: mRNA_coords @@ -9759,9 +9795,11 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp856_c0_seq1', 'gene_id' => '', 'trans_id' => '', + 'orient' => '+', + 'contig' => 'II', + 'asmbl' => 'comp856_c0_seq1', 'coords' => [ [ 3753910, @@ -9771,24 +9809,22 @@ 3754438, '3755057' ] - ], - 'orient' => '+', - 'contig' => 'II' + ] }; - classification: annotated_genes + strand: + com_name: ORF type:complete (+),score=71.94 - is_5prime_partial: 0 - gene_type: protein-coding num_exons: 1 - is_3prime_partial: 0 - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 - gene_length: 1569 + asmbl_id: comp856_c0_seq1 source: transdecoder is_pseudogene: 0 - asmbl_id: comp856_c0_seq1 - strand: + mid_pt: 785 + classification: annotated_genes + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 Model_feat_name: comp856_c0_seq1.p1 + gene_length: 1569 + is_5prime_partial: 0 + gene_type: protein-coding + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9808,7 +9844,10 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', 'gene_id' => '', + 'contig' => 'II', + 'orient' => '-', 'coords' => [ [ 3727877, @@ -9823,25 +9862,22 @@ '3727657' ] ], - 'trans_id' => '', - 'contig' => 'II', - 'orient' => '-', 'asmbl' => 'comp873_c0_seq2' }; - asmbl_id: comp873_c0_seq2 - is_pseudogene: 0 - source: transdecoder + gene_length: 1025 Model_feat_name: comp873_c0_seq2.p1 - mid_pt: 513 - strand: + - is_5prime_partial: 0 gene_type: protein-coding - com_name: ORF type:5prime_partial (+),score=8.59 - classification: annotated_genes - gene_length: 1025 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + is_5prime_partial: 0 is_3prime_partial: 0 + strand: + + com_name: ORF type:5prime_partial (+),score=8.59 + source: transdecoder num_exons: 1 + asmbl_id: comp873_c0_seq2 + is_pseudogene: 0 + mid_pt: 513 + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9865,10 +9901,10 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'contig' => 'III', - 'gene_id' => '', 'trans_id' => '', + 'gene_id' => '', + 'contig' => 'III', + 'orient' => '-', 'coords' => [ [ 1268244, @@ -9881,20 +9917,20 @@ ], 'asmbl' => 'comp888_c0_seq1' }; - gene_type: protein-coding - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=23.94 + mid_pt: 295 classification: annotated_genes - is_3prime_partial: 0 TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 - gene_length: 589 + source: transdecoder + asmbl_id: comp888_c0_seq1 num_exons: 1 is_pseudogene: 0 - asmbl_id: comp888_c0_seq1 - source: transdecoder - Model_feat_name: comp888_c0_seq1.p1 strand: + - mid_pt: 295 + com_name: ORF type:5prime_partial (+),score=23.94 + is_3prime_partial: 0 + gene_type: protein-coding + is_5prime_partial: 0 + gene_length: 589 + Model_feat_name: comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9917,8 +9953,6 @@ Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'asmbl' => 'comp940_c0_seq1', - 'gene_id' => '', - 'trans_id' => '', 'coords' => [ [ 105641, @@ -9930,22 +9964,24 @@ ] ], 'orient' => '+', - 'contig' => 'III' + 'contig' => 'III', + 'gene_id' => '', + 'trans_id' => '' }; - Model_feat_name: comp940_c0_seq1.p1 + com_name: ORF type:complete (+),score=94.37 strand: + - mid_pt: 1065 is_pseudogene: 0 + num_exons: 1 asmbl_id: comp940_c0_seq1 source: transdecoder - is_3prime_partial: 0 + classification: annotated_genes TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + mid_pt: 1065 + Model_feat_name: comp940_c0_seq1.p1 gene_length: 2129 - num_exons: 1 is_5prime_partial: 0 gene_type: protein-coding - com_name: ORF type:complete (+),score=94.37 - classification: annotated_genes + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9965,7 +10001,8 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp983_c0_seq1', + 'trans_id' => '', + 'gene_id' => '', 'coords' => [ [ 4100066, @@ -9976,25 +10013,24 @@ '4100014' ] ], - 'trans_id' => '', - 'gene_id' => '', - 'orient' => '-', - 'contig' => 'I' + 'asmbl' => 'comp983_c0_seq1', + 'contig' => 'I', + 'orient' => '-' }; - is_pseudogene: 0 - asmbl_id: comp983_c0_seq1 - source: transdecoder + gene_length: 1870 Model_feat_name: comp983_c0_seq1.p1 - strand: + - mid_pt: 935 gene_type: protein-coding is_5prime_partial: 0 - classification: annotated_genes - com_name: ORF type:5prime_partial (+),score=143.65 is_3prime_partial: 0 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 - gene_length: 1870 + com_name: ORF type:5prime_partial (+),score=143.65 + strand: + + is_pseudogene: 0 + source: transdecoder + asmbl_id: comp983_c0_seq1 num_exons: 1 + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + classification: annotated_genes + mid_pt: 935 gene_synonyms: mRNA_coords CDS_coords @@ -10038,7 +10074,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Sat Sep 26 05:33:28 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Mon Aug 25 01:20:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -10063,8 +10099,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Sat Sep 26 05:33:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Sat Sep 26 05:33:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Mon Aug 25 01:20:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Mon Aug 25 01:20:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: NM_198270.p1, not unique enough -skipping training candidate: NR_104391.p1, not unique enough -skipping training candidate: NR_104395.p1, not unique enough @@ -12682,37 +12718,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Sat Sep 26 05:33:50 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Mon Aug 25 01:20:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Sat Sep 26 05:33:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores -* [Sat Sep 26 05:33:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat Sep 26 05:34:25 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Mon Aug 25 01:20:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores +* [Mon Aug 25 01:20:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Mon Aug 25 01:20:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat Sep 26 05:34:26 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sat Sep 26 05:34:26 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sat Sep 26 05:34:28 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Mon Aug 25 01:20:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Mon Aug 25 01:20:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Mon Aug 25 01:20:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:35:11 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:21:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat Sep 26 05:35:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Mon Aug 25 01:21:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:35:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:21:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat Sep 26 05:35:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Mon Aug 25 01:21:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:35:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Mon Aug 25 01:21:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:35:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Mon Aug 25 01:21:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 336 num_incorporate: 100 -feature swap of score: 3.78911079353454 instead of -4.15762669956 -feature swap of score: 4.3075564869904 instead of -3.54241712691985 @@ -12815,33 +12851,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Sat Sep 26 05:35:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Mon Aug 25 01:21:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:35:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:21:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat Sep 26 05:35:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Mon Aug 25 01:21:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:35:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:21:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat Sep 26 05:35:55 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Mon Aug 25 01:21:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:35:55 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Mon Aug 25 01:21:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 -* [Sat Sep 26 05:35:57 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Sat Sep 26 05:35:57 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed +* [Mon Aug 25 01:21:48 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Mon Aug 25 01:21:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Sat Sep 26 05:35:57 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep +* [Mon Aug 25 01:21:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Sat Sep 26 05:35:59 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds +* [Mon Aug 25 01:21:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* @@ -12953,7 +12989,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Sat Sep 26 05:36:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Mon Aug 25 01:21:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -12977,15 +13013,15 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Sat Sep 26 05:36:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Sat Sep 26 05:36:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr --skipping training candidate: bdg_i4.p1, not unique enough +* [Mon Aug 25 01:21:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Mon Aug 25 01:21:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +-skipping training candidate: bdg_i3.p1, not unique enough -skipping training candidate: bdg_i2.p1, not unique enough -skipping training candidate: bdg_i1.p1, not unique enough -skipping training candidate: Dgk_i7.p1, not unique enough -skipping training candidate: Cdep_i1.p1, not unique enough --skipping training candidate: eIF5B_i3.p1, not unique enough -skipping training candidate: eIF5B_i2.p1, not unique enough +-skipping training candidate: eIF5B_i4.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough -skipping training candidate: Dgk_i6.p1, not unique enough @@ -12995,25 +13031,25 @@ -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i3.p1, not unique enough +-skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough +-skipping training candidate: Calx_i4.p1, not unique enough +-skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: Calx_i5.p1, not unique enough --skipping training candidate: Calx_i1.p1, not unique enough --skipping training candidate: Calx_i4.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough --skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough +-skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: Klp10A_i5.p1, not unique enough --skipping training candidate: Klp10A_i6.p1, not unique enough -skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough +-skipping training candidate: Klp10A_i1.p1, not unique enough -skipping training candidate: Klp10A_i2.p1, not unique enough --skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough +-skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough -skipping training candidate: CG33970_i1.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough @@ -13022,13 +13058,13 @@ -skipping training candidate: CG10082_i2.p1, not unique enough -skipping training candidate: CG12581_i2.p1, not unique enough -skipping training candidate: CG6091_i3.p1, not unique enough --skipping training candidate: hrg_i4.p1, not unique enough --skipping training candidate: hrg_i3.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough +-skipping training candidate: hrg_i3.p1, not unique enough +-skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough --skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough +-skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough @@ -13041,45 +13077,45 @@ -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough --skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Aldh-III_i12.p1, not unique enough --skipping training candidate: Hsc70-1_i3.p1, not unique enough +-skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough +-skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Est-6_i1.p1, not unique enough +-skipping training candidate: S-Lap3_i1.p1, not unique enough -skipping training candidate: S-Lap3_i3.p1, not unique enough --skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough --skipping training candidate: CG30438_i5.p1, not unique enough -skipping training candidate: CG30438_i3.p1, not unique enough --skipping training candidate: CG30438_i1.p1, not unique enough +-skipping training candidate: CG30438_i2.p1, not unique enough +-skipping training candidate: CG30438_i5.p1, not unique enough -skipping training candidate: CG6145_i4.p1, not unique enough -skipping training candidate: CG33970_i3.p1, not unique enough -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough +-skipping training candidate: Eno_i5.p1, not unique enough -skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i3.p1, not unique enough --skipping training candidate: Eno_i1.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough --skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i7.p1, not unique enough --skipping training candidate: Aldh-III_i4.p1, not unique enough --skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Aldh-III_i6.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough +-skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough --skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough +-skipping training candidate: Eno_i1.p2, not unique enough +-skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough --skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough --skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: CG6424_i4.p2, not unique enough --skipping training candidate: CG6424_i2.p2, not unique enough -skipping training candidate: CG6424_i3.p2, not unique enough +-skipping training candidate: CG6424_i1.p2, not unique enough +-skipping training candidate: CG6424_i2.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough @@ -13087,28 +13123,28 @@ -skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i4.p1, not unique enough -skipping training candidate: AdipoR_i2.p1, not unique enough --skipping training candidate: AdipoR_i3.p1, not unique enough --skipping training candidate: Tm1_i5.p1, not unique enough +-skipping training candidate: AdipoR_i5.p1, not unique enough +-skipping training candidate: AdipoR_i4.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough +-skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough --skipping training candidate: kto_i1.p2, not unique enough +-skipping training candidate: kto_i2.p3, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough --skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough --skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: CG8136_i1.p1, not unique enough +-skipping training candidate: CG8136_i3.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough --skipping training candidate: CG7564_i4.p1, not unique enough +-skipping training candidate: CG7564_i1.p1, not unique enough -skipping training candidate: CG7564_i2.p3, not unique enough --skipping training candidate: CG7564_i3.p1, not unique enough +-skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough --skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i5.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough +-skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough @@ -13116,135 +13152,135 @@ -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough +-skipping training candidate: ogre_i1.p1, not unique enough +-skipping training candidate: ogre_i6.p1, not unique enough +-skipping training candidate: ogre_i3.p1, not unique enough -skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: ogre_i2.p1, not unique enough --skipping training candidate: ogre_i3.p1, not unique enough --skipping training candidate: ogre_i4.p1, not unique enough --skipping training candidate: ogre_i1.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough -skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough --skipping training candidate: CG13284_i3.p1, not unique enough +-skipping training candidate: CG13284_i5.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough --skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: CG13284_i4.p1, not unique enough +-skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough -skipping training candidate: Klp10A_i5.p2, not unique enough --skipping training candidate: Klp10A_i6.p2, not unique enough -skipping training candidate: Klp10A_i3.p2, not unique enough -skipping training candidate: Klp10A_i4.p2, not unique enough +-skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough --skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough +-skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough -skipping training candidate: regucalcin_i4.p1, not unique enough -skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough +-skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: l(3)05822_i3.p2, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough --skipping training candidate: l(3)05822_i2.p2, not unique enough +-skipping training candidate: Tm1_i2.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough +-skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Tm1_i2.p1, not unique enough --skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough --skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Tm1_i11.p1, not unique enough +-skipping training candidate: Npl4_i2.p2, not unique enough -skipping training candidate: Npl4_i3.p2, not unique enough --skipping training candidate: Npl4_i1.p2, not unique enough +-skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough -skipping training candidate: Sec16_i1.p2, not unique enough --skipping training candidate: Sec16_i5.p2, not unique enough --skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough --skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.p2, not unique enough --skipping training candidate: eIF5B_i1.p2, not unique enough +-skipping training candidate: CG8312_i4.p2, not unique enough +-skipping training candidate: Dgk_i7.p2, not unique enough -skipping training candidate: eIF5B_i3.p2, not unique enough -skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: eIF5B_i4.p2, not unique enough +-skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: Dgk_i6.p2, not unique enough --skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: l(1)G0193_i2.p2, not unique enough +-skipping training candidate: Dgk_i3.p2, not unique enough +-skipping training candidate: l(1)G0193_i1.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough --skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough +-skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough -skipping training candidate: Dgk_i6.p3, not unique enough --skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough +-skipping training candidate: l(3)05822_i4.p3, not unique enough -skipping training candidate: l(3)05822_i3.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough --skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i2.p2, not unique enough --skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough +-skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough --skipping training candidate: CG13887_i2.p1, not unique enough +-skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG14995_i7.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough -skipping training candidate: nmo_i1.p2, not unique enough --skipping training candidate: nmo_i7.p2, not unique enough +-skipping training candidate: nmo_i2.p2, not unique enough -skipping training candidate: nmo_i6.p2, not unique enough -skipping training candidate: nmo_i3.p2, not unique enough --skipping training candidate: nmo_i5.p2, not unique enough --skipping training candidate: nmo_i2.p2, not unique enough +-skipping training candidate: nmo_i4.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough +-skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: gukh_i4.p3, not unique enough --skipping training candidate: gukh_i1.p2, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough --skipping training candidate: RpL15_i1.p1, not unique enough --skipping training candidate: RpL15_i4.p1, not unique enough --skipping training candidate: RpL15_i3.p1, not unique enough -skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough +-skipping training candidate: RpL15_i4.p1, not unique enough +-skipping training candidate: RpL15_i3.p1, not unique enough +-skipping training candidate: RpL15_i1.p1, not unique enough +-skipping training candidate: Npl4_i2.p3, not unique enough -skipping training candidate: Npl4_i3.p3, not unique enough --skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: trc_i2.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p3, not unique enough --skipping training candidate: Hsc70-1_i2.p3, not unique enough +-skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough --skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: CG10237_i1.p2, not unique enough -skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: CG10237_i5.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: Eno_i6.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Eno_i5.p3, not unique enough -skipping training candidate: Eno_i4.p3, not unique enough --skipping training candidate: Eno_i6.p3, not unique enough -skipping training candidate: Eno_i3.p3, not unique enough --skipping training candidate: Eno_i1.p3, not unique enough +-skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: Sec16_i1.p3, not unique enough --skipping training candidate: Sec16_i4.p3, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough -skipping training candidate: gukh_i2.p2, not unique enough --skipping training candidate: ATPsyn-d_i1.p1, not unique enough -skipping training candidate: ATPsyn-d_i3.p1, not unique enough --skipping training candidate: CG10082_i2.p2, not unique enough +-skipping training candidate: ATPsyn-d_i1.p1, not unique enough +-skipping training candidate: CG10082_i1.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough --skipping training candidate: CG30438_i5.p2, not unique enough --skipping training candidate: CG30438_i3.p2, not unique enough +-skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG30438_i1.p2, not unique enough --skipping training candidate: CG30438_i4.p2, not unique enough +-skipping training candidate: CG30438_i3.p2, not unique enough +-skipping training candidate: CG30438_i2.p2, not unique enough +-skipping training candidate: CG30438_i5.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough -skipping training candidate: cdi_i2.p2, not unique enough @@ -13252,299 +13288,299 @@ -skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i1.p1, not unique enough --skipping training candidate: ADD1_i3.p2, not unique enough +-skipping training candidate: ADD1_i2.p2, not unique enough +-skipping training candidate: Sec16_i3.p3, not unique enough -skipping training candidate: Sec16_i1.p4, not unique enough --skipping training candidate: Sec16_i4.p4, not unique enough -skipping training candidate: bic_i1.p1, not unique enough -skipping training candidate: CG12581_i2.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i4.p1, not unique enough --skipping training candidate: ctp_i1.p1, not unique enough -skipping training candidate: ctp_i3.p1, not unique enough --skipping training candidate: hrg_i4.p2, not unique enough +-skipping training candidate: ctp_i2.p1, not unique enough +-skipping training candidate: ctp_i1.p1, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough +-skipping training candidate: hrg_i4.p2, not unique enough +-skipping training candidate: Eno_i6.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Eno_i5.p4, not unique enough -skipping training candidate: Eno_i4.p4, not unique enough --skipping training candidate: Eno_i6.p4, not unique enough -skipping training candidate: Eno_i3.p4, not unique enough --skipping training candidate: Eno_i1.p4, not unique enough -skipping training candidate: Klp10A_i5.p3, not unique enough --skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Klp10A_i2.p4, not unique enough --skipping training candidate: Calx_i3.p2, not unique enough +-skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Calx_i6.p2, not unique enough +-skipping training candidate: Calx_i3.p2, not unique enough -skipping training candidate: Calx_i2.p2, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough --skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i9.p2, not unique enough --skipping training candidate: Calx_i4.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough --skipping training candidate: CG7564_i4.p2, not unique enough --skipping training candidate: CG7564_i4.p3, not unique enough +-skipping training candidate: CG7564_i1.p3, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough -skipping training candidate: CG7564_i2.p5, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough +-skipping training candidate: CG7564_i4.p2, not unique enough +-skipping training candidate: CG7564_i4.p3, not unique enough -skipping training candidate: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.p3, not unique enough --skipping training candidate: eIF5B_i1.p3, not unique enough -skipping training candidate: eIF5B_i3.p3, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i4.p3, not unique enough +-skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough --skipping training candidate: AdipoR_i3.p2, not unique enough --skipping training candidate: CG6424_i4.p3, not unique enough --skipping training candidate: CG6424_i2.p3, not unique enough +-skipping training candidate: AdipoR_i4.p2, not unique enough -skipping training candidate: CG6424_i3.p3, not unique enough --skipping training candidate: CG6424_i3.p4, not unique enough --skipping training candidate: Tm1_i16.p2, not unique enough --skipping training candidate: Tm1_i13.p2, not unique enough +-skipping training candidate: CG6424_i1.p3, not unique enough +-skipping training candidate: CG6424_i1.p4, not unique enough +-skipping training candidate: CG6424_i2.p3, not unique enough -skipping training candidate: Tm1_i14.p2, not unique enough +-skipping training candidate: Tm1_i5.p2, not unique enough +-skipping training candidate: Tm1_i16.p2, not unique enough -skipping training candidate: Dgk_i6.p4, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough -skipping training candidate: Dgk_i2.p5, not unique enough --skipping training candidate: Dgk_i1.p4, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i7.p5, not unique enough -skipping training candidate: cdi_i2.p3, not unique enough -skipping training candidate: eff_i1.p1, not unique enough --skipping training candidate: eff_i2.p1, not unique enough +-skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i5.p4, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i3.p4, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough --skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: eIF5B_i4.p5, not unique enough +-skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: Sec16_i5.p4, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough --skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough --skipping training candidate: Sec16_i5.p4, not unique enough --skipping training candidate: CG32082_i4.p2, not unique enough --skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: CG32082_i3.p2, not unique enough +-skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough -skipping training candidate: CG3530_i2.p2, not unique enough -skipping training candidate: CG3530_i1.p2, not unique enough --skipping training candidate: Dgk_i2.p6, not unique enough +-skipping training candidate: Dgk_i7.p6, not unique enough +-skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough --skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: sqd_i1.p2, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: CG7564_i2.p6, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough +-skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: S-Lap3_i1.p2, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough --skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: cdi_i2.p4, not unique enough --skipping training candidate: CG6091_i1.p2, not unique enough --skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough +-skipping training candidate: CG6091_i3.p2, not unique enough +-skipping training candidate: CG6091_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough --skipping training candidate: Cnx99A_i4.p2, not unique enough --skipping training candidate: Cnx99A_i2.p2, not unique enough -skipping training candidate: Cnx99A_i3.p2, not unique enough +-skipping training candidate: Cnx99A_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i2.p2, not unique enough +-skipping training candidate: Sec16_i5.p5, not unique enough -skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: Sec16_i1.p6, not unique enough --skipping training candidate: Sec16_i5.p5, not unique enough -skipping training candidate: ogre_i3.p2, not unique enough -skipping training candidate: CG6024_i2.p3, not unique enough -skipping training candidate: hrg_i3.p3, not unique enough --skipping training candidate: hrg_i1.p3, not unique enough --skipping training candidate: ATPsyn-d_i3.p2, not unique enough --skipping training candidate: CG6091_i1.p3, not unique enough +-skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: ATPsyn-d_i1.p2, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough +-skipping training candidate: CG6091_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough --skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: CG33970_i3.p2, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: Aldh-III_i8.p2, not unique enough -skipping training candidate: Aldh-III_i11.p2, not unique enough --skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i1.p2, not unique enough --skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough -skipping training candidate: CG13284_i4.p2, not unique enough +-skipping training candidate: CG13284_i5.p2, not unique enough +-skipping training candidate: CG13284_i2.p2, not unique enough -skipping training candidate: Lip4_i1.p2, not unique enough --skipping training candidate: Lip4_i3.p2, not unique enough +-skipping training candidate: Lip4_i2.p2, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough --skipping training candidate: Dgk_i5.p4, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough --skipping training candidate: Tm1_i16.p3, not unique enough --skipping training candidate: Tm1_i13.p3, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough -skipping training candidate: Tm1_i14.p3, not unique enough --skipping training candidate: CG8312_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough --skipping training candidate: CG8312_i3.p3, not unique enough --skipping training candidate: CG8312_i3.p4, not unique enough +-skipping training candidate: Tm1_i5.p3, not unique enough +-skipping training candidate: Tm1_i16.p3, not unique enough -skipping training candidate: CG8312_i2.p3, not unique enough -skipping training candidate: CG8312_i2.p4, not unique enough +-skipping training candidate: CG8312_i3.p3, not unique enough +-skipping training candidate: CG8312_i3.p4, not unique enough +-skipping training candidate: CG8312_i4.p3, not unique enough +-skipping training candidate: CG8312_i4.p4, not unique enough -skipping training candidate: Klp10A_i5.p4, not unique enough --skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: Klp10A_i1.p4, not unique enough -skipping training candidate: Klp10A_i2.p6, not unique enough -skipping training candidate: eff_i1.p2, not unique enough --skipping training candidate: eff_i2.p2, not unique enough --skipping training candidate: CG14995_i4.p4, not unique enough +-skipping training candidate: eff_i3.p2, not unique enough +-skipping training candidate: CG14995_i1.p4, not unique enough -skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough --skipping training candidate: CG14995_i1.p4, not unique enough -skipping training candidate: CG14995_i5.p5, not unique enough --skipping training candidate: CG6424_i4.p4, not unique enough --skipping training candidate: CG6424_i2.p4, not unique enough +-skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG6424_i3.p5, not unique enough +-skipping training candidate: CG6424_i1.p5, not unique enough +-skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG12581_i2.p3, not unique enough --skipping training candidate: CG32082_i4.p5, not unique enough --skipping training candidate: CG32082_i1.p3, not unique enough -skipping training candidate: CG32082_i3.p3, not unique enough +-skipping training candidate: CG32082_i1.p3, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough +-skipping training candidate: Cnx99A_i1.p3, not unique enough -skipping training candidate: Cnx99A_i2.p3, not unique enough --skipping training candidate: Cnx99A_i3.p3, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough --skipping training candidate: Cdep_i2.p6, not unique enough +-skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough --skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: CG33970_i3.p3, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: CG33970_i1.p3, not unique enough +-skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough --skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough --skipping training candidate: Sec16_i5.p6, not unique enough +-skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: mge_i3.p1, not unique enough -skipping training candidate: CG6024_i2.p4, not unique enough --skipping training candidate: Myo61F_i2.p2, not unique enough --skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Myo61F_i1.p2, not unique enough +-skipping training candidate: Myo61F_i3.p2, not unique enough +-skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough +-skipping training candidate: Cnx99A_i1.p4, not unique enough -skipping training candidate: Cnx99A_i2.p4, not unique enough --skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG13887_i2.p2, not unique enough --skipping training candidate: CG6145_i5.p2, not unique enough --skipping training candidate: CG6145_i1.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough +-skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG6145_i2.p2, not unique enough --skipping training candidate: Calx_i3.p3, not unique enough +-skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG6145_i4.p2, not unique enough +-skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: Calx_i6.p3, not unique enough +-skipping training candidate: Calx_i3.p3, not unique enough -skipping training candidate: Calx_i2.p3, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough --skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i4.p3, not unique enough --skipping training candidate: mge_i2.p2, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough +-skipping training candidate: mge_i1.p2, not unique enough +-skipping training candidate: AdipoR_i1.p2, not unique enough +-skipping training candidate: AdipoR_i2.p2, not unique enough -skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i4.p3, not unique enough --skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: AdipoR_i3.p3, not unique enough --skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough --skipping training candidate: Aldh-III_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i9.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough --skipping training candidate: Cdep_i4.p3, not unique enough --skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i2.p9, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough --skipping training candidate: hrg_i3.p4, not unique enough +-skipping training candidate: Cdep_i3.p4, not unique enough +-skipping training candidate: Cdep_i4.p3, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough +-skipping training candidate: hrg_i3.p4, not unique enough +-skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i2.p4, not unique enough --skipping training candidate: Sec16_i3.p7, not unique enough --skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i5.p7, not unique enough +-skipping training candidate: Sec16_i5.p8, not unique enough -skipping training candidate: Sec16_i2.p8, not unique enough -skipping training candidate: Sec16_i2.p9, not unique enough --skipping training candidate: Sec16_i1.p8, not unique enough --skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Sec16_i4.p8, not unique enough -skipping training candidate: Sec16_i4.p9, not unique enough --skipping training candidate: Sec16_i5.p7, not unique enough --skipping training candidate: Sec16_i5.p8, not unique enough +-skipping training candidate: Sec16_i3.p7, not unique enough +-skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i1.p8, not unique enough +-skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough --skipping training candidate: CG6091_i1.p4, not unique enough --skipping training candidate: CG6091_i3.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough +-skipping training candidate: CG6091_i3.p4, not unique enough +-skipping training candidate: CG6091_i4.p4, not unique enough -skipping training candidate: CanB2_i1.p2, not unique enough -skipping training candidate: IP3K1_i1.p3, not unique enough -skipping training candidate: Klp10A_i5.p5, not unique enough --skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i3.p5, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough +-skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough --skipping training candidate: Cdep_i4.p4, not unique enough --skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i2.p10, not unique enough +-skipping training candidate: Cdep_i3.p5, not unique enough +-skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Est-6_i1.p2, not unique enough -skipping training candidate: Klp10A_i5.p6, not unique enough --skipping training candidate: Klp10A_i6.p6, not unique enough -skipping training candidate: Klp10A_i3.p6, not unique enough -skipping training candidate: Klp10A_i4.p6, not unique enough +-skipping training candidate: Klp10A_i1.p7, not unique enough -skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough --skipping training candidate: ADD1_i3.p4, not unique enough +-skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i4.p3, not unique enough --skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough --skipping training candidate: Myo61F_i2.p3, not unique enough --skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Cnx99A_i1.p5, not unique enough +-skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Myo61F_i1.p3, not unique enough --skipping training candidate: Myo61F_i2.p4, not unique enough --skipping training candidate: Myo61F_i4.p4, not unique enough +-skipping training candidate: Myo61F_i3.p3, not unique enough +-skipping training candidate: Myo61F_i4.p3, not unique enough -skipping training candidate: Myo61F_i1.p4, not unique enough +-skipping training candidate: Myo61F_i3.p4, not unique enough +-skipping training candidate: Myo61F_i4.p4, not unique enough -skipping training candidate: bic_i1.p3, not unique enough --skipping training candidate: CG10082_i2.p3, not unique enough --skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: CG10082_i1.p5, not unique enough -skipping training candidate: CG32082_i3.p4, not unique enough +-skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough +-skipping training candidate: Eno_i6.p5, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Eno_i5.p6, not unique enough -skipping training candidate: Eno_i4.p6, not unique enough --skipping training candidate: Eno_i6.p5, not unique enough -skipping training candidate: Eno_i3.p5, not unique enough --skipping training candidate: Eno_i1.p6, not unique enough +-skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough --skipping training candidate: Sec16_i4.p10, not unique enough +-skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: Dgk_i2.p8, not unique enough --skipping training candidate: Dgk_i5.p5, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough --skipping training candidate: nmo_i6.p3, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: nmo_i4.p3, not unique enough -skipping training candidate: CG33970_i1.p4, not unique enough -skipping training candidate: sqd_i3.p2, not unique enough +-skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: Dgk_i3.p7, not unique enough --skipping training candidate: Dgk_i1.p7, not unique enough --skipping training candidate: His4r_i4.p1, not unique enough --skipping training candidate: His4r_i3.p1, not unique enough -skipping training candidate: His4r_i2.p1, not unique enough +-skipping training candidate: His4r_i3.p1, not unique enough +-skipping training candidate: His4r_i1.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p4, not unique enough --skipping training candidate: Hsc70-1_i2.p5, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: hrg_i3.p5, not unique enough --skipping training candidate: hrg_i1.p5, not unique enough +-skipping training candidate: hrg_i4.p6, not unique enough -skipping training candidate: CG8136_i2.p2, not unique enough --skipping training candidate: CG8136_i4.p2, not unique enough -skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: Myo61F_i2.p5, not unique enough --skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: CG8136_i3.p2, not unique enough -skipping training candidate: Myo61F_i1.p5, not unique enough --skipping training candidate: CG6091_i1.p5, not unique enough --skipping training candidate: CG6091_i3.p5, not unique enough +-skipping training candidate: Myo61F_i3.p5, not unique enough +-skipping training candidate: Myo61F_i4.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough --skipping training candidate: CG6145_i5.p3, not unique enough --skipping training candidate: CG6145_i1.p3, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: CG6091_i3.p5, not unique enough +-skipping training candidate: CG6091_i4.p5, not unique enough -skipping training candidate: CG6145_i2.p3, not unique enough +-skipping training candidate: CG6145_i1.p3, not unique enough +-skipping training candidate: CG6145_i5.p3, not unique enough +-skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: gukh_i2.p3, not unique enough -skipping training candidate: sqd_i3.p3, not unique enough -skipping training candidate: CG33125_i1.p4, not unique enough @@ -13552,121 +13588,120 @@ -redundancy-minimized set includes 286 / 856 = 33.41% -* [Sat Sep 26 05:36:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Mon Aug 25 01:21:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 49.4 -* [Sat Sep 26 05:36:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Sat Sep 26 05:36:11 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat Sep 26 05:36:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Mon Aug 25 01:21:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Mon Aug 25 01:21:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Mon Aug 25 01:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat Sep 26 05:36:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sat Sep 26 05:36:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sat Sep 26 05:36:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Mon Aug 25 01:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Mon Aug 25 01:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Mon Aug 25 01:22:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:36:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:22:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat Sep 26 05:36:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Mon Aug 25 01:22:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:36:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Mon Aug 25 01:22:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat Sep 26 05:36:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Mon Aug 25 01:22:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:36:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Mon Aug 25 01:22:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:36:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Mon Aug 25 01:22:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 253 num_incorporate: 75 --feature swap of score: -1.42616949176538 instead of -3.31810280727654 --feature swap of score: -1.23102075718095 instead of -3.34279250327349 --feature swap of score: -1.9392742720726 instead of -2.95012899124158 --feature swap of score: -1.39377765172055 instead of -1.87212517196266 --feature swap of score: -1.00549860875071 instead of -1.21900527838834 --feature swap of score: -0.680136621141599 instead of -0.957884620228475 --feature swap of score: 1.75829410284842 instead of -0.840155121748637 --feature swap of score: -0.919944508547283 instead of -2.34629895635327 --feature swap of score: 2.67114875461627 instead of -1.58360912320071 --feature swap of score: 1.29735791699963 instead of -1.20963885170126 --feature swap of score: -0.490876281820394 instead of -1.44138418406479 --feature swap of score: -0.00572380202004255 instead of -1.31089387566476 --feature swap of score: 0.602969518232938 instead of -1.26912680693986 --feature swap of score: 1.92878586614544 instead of -1.1694412628652 --feature swap of score: 0.738934666604848 instead of -0.956370536900942 --feature swap of score: -0.343358975524356 instead of -1.10703162179499 --feature swap of score: 1.1390575082332 instead of -1.01589682231509 --feature swap of score: -0.149304880951577 instead of -0.864087450370054 --feature swap of score: -0.734491433211705 instead of -0.931903355219247 --feature swap of score: 0.318821551317133 instead of -0.594052293167204 --feature swap of score: 3.15143652318411 instead of -0.328727892164231 --feature swap of score: 1.57433670129486 instead of -0.254715392321584 --feature swap of score: 2.85772301230032 instead of -0.161314866311591 --feature swap of score: 0.155080053116088 instead of -0.036781163423617 --feature swap of score: 2.46724436245325 instead of -0.242700589520046 --feature swap of score: 2.06695198686135 instead of -0.324863499408637 --feature swap of score: 1.515171094715 instead of 0.0544493357286563 --feature swap of score: 1.48156449739072 instead of -0.065455379920518 --feature swap of score: 0.423966293459964 instead of -0.177718538901198 --feature swap of score: 1.08723622304166 instead of -0.498227176906355 --feature swap of score: 1.47047839040819 instead of -0.287833265034744 --feature swap of score: 0.534684247556956 instead of -0.393317421485841 --feature swap of score: 1.70945681264189 instead of -0.470784053807281 --feature swap of score: 2.57662380076941 instead of -0.396710389525443 --feature swap of score: 0.963999748727007 instead of -0.202281218786397 --feature swap of score: 1.56479612814642 instead of 0.0172368261531429 --feature swap of score: 1.01895964951616 instead of -0.113308642294222 --feature swap of score: 0.0901606849998985 instead of -0.628798786848762 --feature swap of score: 2.83708352183625 instead of -0.0600872371055552 --feature swap of score: 0.443696797508059 instead of -0.155087550869685 --feature swap of score: 1.84870541691352 instead of 0.15501604422543 --feature swap of score: 0.61755906170584 instead of 0.265069272681179 --feature swap of score: 2.93739053780928 instead of 0.324770846272802 --feature swap of score: 0.762968505355006 instead of 0.115617992092814 --feature swap of score: 1.70618502141341 instead of 0.495896220318438 --feature swap of score: 1.27521146614292 instead of 0.459834269561304 --feature swap of score: 2.60595701227768 instead of 0.514213492832837 --feature swap of score: 2.20668500309723 instead of 0.328636299946226 --feature swap of score: 1.77163640419881 instead of 0.166683689263103 --feature swap of score: 2.47942939723998 instead of 0.329099182037467 --feature swap of score: 4.5695680896262 instead of 0.565325731885299 --feature swap of score: 1.02938011845137 instead of 0.666933781257795 --feature swap of score: 2.69009356044574 instead of 0.720828618826253 --feature swap of score: 6.51074259621129 instead of 0.00265659822439274 --feature swap of score: 2.99886760685055 instead of 0.439658608549701 --num feature swaps: 55 -* [Sat Sep 26 05:36:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +-feature swap of score: -1.4984004401557 instead of -3.53337571338455 +-feature swap of score: -1.3258885477831 instead of -3.42198439991653 +-feature swap of score: -1.67490261600074 instead of -3.03442527127545 +-feature swap of score: -1.48906817741182 instead of -1.50244302238483 +-feature swap of score: -0.636573305388198 instead of -1.05553407990358 +-feature swap of score: 1.95056428727654 instead of -1.09719296710193 +-feature swap of score: -0.593468631867452 instead of -1.04222406608578 +-feature swap of score: 2.73857660980429 instead of -0.932485178359621 +-feature swap of score: -0.540922539993657 instead of -1.00779482382887 +-feature swap of score: 2.38860986639845 instead of -1.00527694318106 +-feature swap of score: -0.299469020508784 instead of -0.873366699428201 +-feature swap of score: 0.533577681526708 instead of -1.01142385926735 +-feature swap of score: 1.70057076991751 instead of -1.04597087562816 +-feature swap of score: 1.29352600955616 instead of -1.37400587977437 +-feature swap of score: -0.810154428773248 instead of -0.939676681832002 +-feature swap of score: -0.00579778196408232 instead of -0.856103983905413 +-feature swap of score: -0.561907908015051 instead of -1.12391710260962 +-feature swap of score: 1.47809107510804 instead of -0.422178585776763 +-feature swap of score: 2.94977820082149 instead of -0.553480710819251 +-feature swap of score: 1.67426472998169 instead of -0.403692874680551 +-feature swap of score: 1.10010636283429 instead of -2.0343299333927 +-feature swap of score: 2.92842864922573 instead of -0.420327180851423 +-feature swap of score: 0.144024980103518 instead of -0.490944371488407 +-feature swap of score: 2.68354409096057 instead of -0.951358988802818 +-feature swap of score: 1.03650518106604 instead of -0.753891712028202 +-feature swap of score: 2.00443115704687 instead of -0.663327033722159 +-feature swap of score: -0.762643464931068 instead of -0.805188145623719 +-feature swap of score: 0.931908087967997 instead of -0.723932181337403 +-feature swap of score: 2.61848706161758 instead of -0.685608121952256 +-feature swap of score: 0.277851521755255 instead of -0.793963463284238 +-feature swap of score: 1.23262242681864 instead of -0.94692581101276 +-feature swap of score: 0.255693116427963 instead of -0.939186284081027 +-feature swap of score: 0.527696865970169 instead of -0.56238665176273 +-feature swap of score: 0.884434646320653 instead of -0.44002429750523 +-feature swap of score: 0.412413860782572 instead of -0.339939480404657 +-feature swap of score: -0.100724868924492 instead of -0.763246876368213 +-feature swap of score: 0.519815634002131 instead of -0.270745128145494 +-feature swap of score: 1.58340537112671 instead of -0.149509268010925 +-feature swap of score: 1.03864038572646 instead of 0.116550935897921 +-feature swap of score: 1.14189664413073 instead of 0.033408546752299 +-feature swap of score: 1.32266002407199 instead of 0.237250382667814 +-feature swap of score: 0.736585298579398 instead of 0.0487225330250331 +-feature swap of score: 0.195874835133266 instead of -0.0718795098912324 +-feature swap of score: 3.09452427714679 instead of -0.122092019099251 +-feature swap of score: 0.00253106029802669 instead of -0.400765397280851 +-feature swap of score: 0.274297438186054 instead of -0.714614493780713 +-feature swap of score: 0.706957101726245 instead of 0.00149015357544047 +-feature swap of score: 2.27287190683963 instead of 0.0274101121291087 +-feature swap of score: 0.155589076708836 instead of 0.11919647094874 +-feature swap of score: 0.570587492876327 instead of -0.0322464949922573 +-feature swap of score: 7.70503498663329 instead of -0.288418226175776 +-feature swap of score: 1.60636916012626 instead of -0.041413468107207 +-feature swap of score: 3.58913012456631 instead of -0.0434923025941043 +-feature swap of score: 9.19946655276518 instead of 0.0482735150203224 +-num feature swaps: 54 +* [Mon Aug 25 01:22:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat Sep 26 05:37:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:22:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat Sep 26 05:37:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Mon Aug 25 01:22:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat Sep 26 05:37:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Mon Aug 25 01:22:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat Sep 26 05:37:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Mon Aug 25 01:23:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat Sep 26 05:37:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Mon Aug 25 01:23:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. --number of revised start positions: 10 -* [Sat Sep 26 05:37:19 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Sat Sep 26 05:37:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed +-number of revised start positions: 12 +* [Mon Aug 25 01:23:01 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Mon Aug 25 01:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Sat Sep 26 05:37:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep +* [Mon Aug 25 01:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep -* [Sat Sep 26 05:37:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds +* [Mon Aug 25 01:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* @@ -13682,9 +13717,9 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. +-Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. @@ -13825,12 +13860,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2326348/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1907934 and its subdirectories -I: Current time: Sat Sep 26 05:37:39 -12 2026 -I: pbuilder-time-stamp: 1790444259 +I: removing directory /srv/workspace/pbuilder/2326348 and its subdirectories +I: Current time: Mon Aug 25 01:23:15 +14 2025 +I: pbuilder-time-stamp: 1756034595