Diff of the two buildlogs: -- --- b1/build.log 2025-09-16 15:05:03.121052518 +0000 +++ b2/build.log 2025-09-16 15:15:46.885839571 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 16 02:51:05 -12 2025 -I: pbuilder-time-stamp: 1758034265 +I: Current time: Tue Oct 20 11:28:04 +14 2026 +I: pbuilder-time-stamp: 1792445284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2416656/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/820938/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Oct 19 21:28 /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/820938/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/820938/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=40 ' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=42 ' + 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='d0371e510c8f4964ba2b38d782946728' - 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='2416656' - PS1='# ' - PS2='> ' + INVOCATION_ID=ed8c4f4f05a54c3aa21caa6da56d11d8 + 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=820938 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.gHLALJ4e/pbuilderrc_mrc2 --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.gHLALJ4e/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.gHLALJ4e/pbuilderrc_h6iW --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.gHLALJ4e/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2416656/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/820938/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -287,7 +319,7 @@ 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 134 MB in 34s (3931 kB/s) +Fetched 134 MB in 4s (31.1 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 ... 19917 files and directories currently installed.) @@ -847,8 +879,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 16 14:56:26 UTC 2025. -Universal Time is now: Tue Sep 16 14:56:26 UTC 2025. +Local time is now: Mon Oct 19 21:29:14 UTC 2026. +Universal Time is now: Mon Oct 19 21:29:14 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-15) ... @@ -1000,7 +1032,11 @@ 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/820938/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/820938/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 @@ -1022,7 +1058,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j40 test + make -j42 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' @@ -1063,7 +1099,7 @@ ## 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 -* [Tue Sep 16 02:56:41 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 +* [Tue Oct 20 11:29:33 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 -first extracting base frequencies, we'll need them later. @@ -1115,13 +1151,13 @@ fi -Building a new DB, current time: 09/16/2025 02:56:41 +Building a new DB, current time: 10/20/2026 11:29:33 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 0.00761199 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00751281 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1197,7 +1233,7 @@ 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: 1667.63 +# Mc/sec: 1635.95 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1254,8 +1290,8 @@ 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: 1607.38 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1598.49 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1319,8 +1355,8 @@ 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: 2295.42 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2150.77 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1381,7 +1417,7 @@ 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: 2113.93 +# Mc/sec: 2231.84 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1442,7 +1478,7 @@ 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: 832.90 +# Mc/sec: 836.38 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1492,8 +1528,8 @@ 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: 699.90 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 676.34 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1558,7 +1594,7 @@ 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: 2534.69 +# Mc/sec: 2040.24 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1610,8 +1646,8 @@ 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: 748.57 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 761.02 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1662,7 +1698,7 @@ 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: 2293.32 +# Mc/sec: 2153.60 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1718,8 +1754,8 @@ 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: 2201.45 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2247.62 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1808,7 +1844,7 @@ 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: 1821.03 +# Mc/sec: 1789.94 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1893,7 +1929,7 @@ 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: 2099.57 +# Mc/sec: 2145.12 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1950,7 +1986,7 @@ 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: 00:00:00.01 -# Mc/sec: 1085.17 +# Mc/sec: 1086.79 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -2006,8 +2042,8 @@ 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: 1179.66 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1195.43 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2063,8 +2099,8 @@ 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: 3059.86 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3526.08 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2109,7 +2145,7 @@ 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: 2499.33 +# Mc/sec: 2484.16 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2162,7 +2198,7 @@ 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: 3311.81 +# Mc/sec: 3224.96 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2206,8 +2242,8 @@ 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: 2415.93 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2204.38 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2268,7 +2304,7 @@ 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: 1798.40 +# Mc/sec: 1734.19 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2319,7 +2355,7 @@ 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: 1518.85 +# Mc/sec: 1459.28 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2432,7 +2468,7 @@ 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: 1328.65 +# Mc/sec: 1276.29 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2479,7 +2515,7 @@ 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: 2528.55 +# Mc/sec: 2234.91 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2545,8 +2581,8 @@ 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: 2210.98 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2121.16 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2584,8 +2620,8 @@ 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: 4126.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4115.69 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2661,8 +2697,8 @@ 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: 1593.88 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1551.05 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2715,7 +2751,7 @@ 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: 2718.19 +# Mc/sec: 2589.24 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2800,7 +2836,7 @@ 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: 606.79 +# Mc/sec: 599.63 // Query: DLH [M=217] Accession: PF01738.17 @@ -2847,8 +2883,8 @@ 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: 3818.26 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3404.58 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2895,7 +2931,7 @@ 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: 2390.00 +# Mc/sec: 2292.87 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2945,7 +2981,7 @@ 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: 3119.61 +# Mc/sec: 3206.32 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2988,7 +3024,7 @@ 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: 3673.25 +# Mc/sec: 3823.84 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3033,8 +3069,8 @@ 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: 1497.26 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1481.67 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3072,7 +3108,7 @@ 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: 3815.24 +# Mc/sec: 3847.98 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3124,7 +3160,7 @@ 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: 1828.83 +# Mc/sec: 1804.18 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3161,8 +3197,8 @@ 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: 1957.34 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1986.13 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3200,7 +3236,7 @@ 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: 3431.53 +# Mc/sec: 3486.08 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3251,7 +3287,7 @@ 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: 2668.93 +# Mc/sec: 2723.24 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3289,7 +3325,7 @@ 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: 4999.23 +# Mc/sec: 4524.97 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3350,7 +3386,7 @@ 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: 2699.08 +# Mc/sec: 2754.65 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3394,8 +3430,8 @@ 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: 2896.05 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2655.01 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3452,7 +3488,7 @@ 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: 2837.77 +# Mc/sec: 2636.45 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3507,7 +3543,7 @@ 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: 1058.81 +# Mc/sec: 1069.03 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3545,7 +3581,7 @@ 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: 4420.59 +# Mc/sec: 4468.75 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3622,7 +3658,7 @@ 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: 2946.98 +# Mc/sec: 2914.39 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3687,7 +3723,7 @@ 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: 931.26 +# Mc/sec: 931.31 // Query: FPP [M=866] Accession: PF05911.10 @@ -3738,7 +3774,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2414.39 +# Mc/sec: 2458.67 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3791,7 +3827,7 @@ 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: 2810.94 +# Mc/sec: 2695.49 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3915,7 +3951,7 @@ 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: 788.52 +# Mc/sec: 745.99 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3954,7 +3990,7 @@ 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: 2090.61 +# Mc/sec: 1961.17 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4045,7 +4081,7 @@ 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: 00:00:00.01 -# Mc/sec: 957.64 +# Mc/sec: 915.57 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4095,8 +4131,8 @@ 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: 661.81 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 664.60 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4157,7 +4193,7 @@ 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: 1757.90 +# Mc/sec: 1731.73 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4262,7 +4298,7 @@ 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: 1032.11 +# Mc/sec: 1026.21 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4310,7 +4346,7 @@ 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: 2452.24 +# Mc/sec: 2415.60 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4385,7 +4421,7 @@ 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: 1642.46 +# Mc/sec: 1567.23 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4456,7 +4492,7 @@ 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: 2240.66 +# Mc/sec: 2249.03 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4503,8 +4539,8 @@ 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: 1168.17 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1152.88 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4574,8 +4610,8 @@ 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 423.17 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 419.03 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4626,7 +4662,7 @@ 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: 3489.87 +# Mc/sec: 3603.08 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4677,7 +4713,7 @@ 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: 3825.77 +# Mc/sec: 3794.29 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4716,7 +4752,7 @@ 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: 2650.82 +# Mc/sec: 2536.81 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4761,7 +4797,7 @@ 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: 2315.41 +# Mc/sec: 2462.07 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4813,7 +4849,7 @@ 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: 1806.19 +# Mc/sec: 1879.77 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4896,7 +4932,7 @@ 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: 1424.50 +# Mc/sec: 1395.04 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4996,8 +5032,8 @@ 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: 977.61 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 976.16 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5052,7 +5088,7 @@ 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: 1813.96 +# Mc/sec: 1642.01 // Query: IBR [M=62] Accession: PF01485.20 @@ -5090,7 +5126,7 @@ 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: 2167.94 +# Mc/sec: 2123.09 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5138,7 +5174,7 @@ 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: 1448.28 +# Mc/sec: 1374.12 // Query: malic [M=182] Accession: PF00390.18 @@ -5177,7 +5213,7 @@ 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: 5017.21 +# Mc/sec: 4199.15 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5214,8 +5250,8 @@ 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: 1578.44 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1507.16 // Query: MatE [M=161] Accession: PF01554.17 @@ -5299,8 +5335,8 @@ 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: 1722.68 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1554.59 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5337,8 +5373,8 @@ 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: 3898.96 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1896.48 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5512,8 +5548,8 @@ 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 290.45 +# CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06 +# Mc/sec: 171.69 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5555,8 +5591,8 @@ 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: 2561.54 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2485.17 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5612,8 +5648,8 @@ 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: 1423.89 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1435.98 // Query: MIP [M=227] Accession: PF00230.19 @@ -5663,8 +5699,8 @@ 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: 3170.90 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2870.49 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5717,7 +5753,7 @@ 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: 1882.71 +# Mc/sec: 1826.99 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5808,7 +5844,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2722.01 +# Mc/sec: 2635.36 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5846,7 +5882,7 @@ 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: 2409.22 +# Mc/sec: 2289.85 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5883,8 +5919,8 @@ 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: 3757.79 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3892.35 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5937,7 +5973,7 @@ 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: 3062.60 +# Mc/sec: 3048.65 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5975,7 +6011,7 @@ 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: 4277.93 +# Mc/sec: 4335.94 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6095,8 +6131,8 @@ 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1186.95 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1291.42 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6147,7 +6183,7 @@ 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: 2118.56 +# Mc/sec: 3290.10 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6218,7 +6254,7 @@ 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: 2330.86 +# Mc/sec: 2461.51 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6271,7 +6307,7 @@ 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: 1294.36 +# Mc/sec: 1295.77 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6334,7 +6370,7 @@ 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: 1692.33 +# Mc/sec: 2341.37 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6436,8 +6472,8 @@ 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 360.87 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 362.85 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6485,7 +6521,7 @@ 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: 2622.97 +# Mc/sec: 2350.72 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6536,7 +6572,7 @@ 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: 1693.71 +# Mc/sec: 1726.15 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6586,8 +6622,8 @@ 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: 2518.73 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2523.07 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6638,7 +6674,7 @@ 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: 3703.19 +# Mc/sec: 3638.32 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6682,8 +6718,8 @@ 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: 3522.26 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3248.07 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6730,7 +6766,7 @@ 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: 1713.70 +# Mc/sec: 1701.21 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6794,8 +6830,8 @@ 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: 763.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 726.57 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6840,7 +6876,7 @@ 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: 2362.02 +# Mc/sec: 2477.23 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6892,8 +6928,8 @@ 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: 1258.86 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1269.03 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6938,7 +6974,7 @@ 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: 3549.80 +# Mc/sec: 3473.47 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7038,8 +7074,8 @@ 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: 00:00:00.02 -# Mc/sec: 618.55 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 608.12 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7084,7 +7120,7 @@ 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: 1000.74 +# Mc/sec: 915.11 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7137,7 +7173,7 @@ 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: 3145.75 +# Mc/sec: 2974.45 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7210,8 +7246,8 @@ 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: 553.49 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 532.47 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7271,8 +7307,8 @@ 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: 2794.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2645.88 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7317,7 +7353,7 @@ 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: 2987.39 +# Mc/sec: 2762.08 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7370,7 +7406,7 @@ 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: 2913.87 +# Mc/sec: 2745.32 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7408,7 +7444,7 @@ 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: 7037.52 +# Mc/sec: 6575.62 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7450,8 +7486,8 @@ 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: 3805.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3599.72 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7513,8 +7549,8 @@ 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 1005.46 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 975.21 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7552,7 +7588,7 @@ 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: 4349.32 +# Mc/sec: 4116.89 // Query: Usher [M=551] Accession: PF00577.19 @@ -7597,7 +7633,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3406.25 +# Mc/sec: 3181.27 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7644,7 +7680,7 @@ 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: 1097.11 +# Mc/sec: 1021.22 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7689,7 +7725,7 @@ 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: 1063.65 +# Mc/sec: 1063.03 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7734,7 +7770,7 @@ 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: 1159.31 +# Mc/sec: 1114.58 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7789,7 +7825,7 @@ 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: 1306.96 +# Mc/sec: 1246.47 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7828,7 +7864,7 @@ 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: 845.45 +# Mc/sec: 809.28 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7880,7 +7916,7 @@ 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: 1208.15 +# Mc/sec: 1111.07 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7928,7 +7964,7 @@ 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: 1940.79 +# Mc/sec: 1901.84 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7966,15 +8002,15 @@ 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: 1564.56 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1630.17 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Tue Sep 16 02:56:43 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 -* [Tue Sep 16 02:56:43 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 +* [Tue Oct 20 11:29:35 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 +* [Tue Oct 20 11:29:35 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 -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 @@ -8001,39 +8037,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Tue Sep 16 02:56:43 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 +* [Tue Oct 20 11:29:35 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 PCT_GC: 37 -* [Tue Sep 16 02:56:43 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 -* [Tue Sep 16 02:56:44 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 -* [Tue Sep 16 02:56:44 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 +* [Tue Oct 20 11:29:35 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 +* [Tue Oct 20 11:29:35 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 +* [Tue Oct 20 11:29:36 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 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Tue Sep 16 02:56:44 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* [Tue Sep 16 02:56:44 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 -* [Tue Sep 16 02:56:44 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 +* [Tue Oct 20 11:29:36 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* [Tue Oct 20 11:29:36 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 +* [Tue Oct 20 11:29:36 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/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 -* [Tue Sep 16 02:57:02 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 +* [Tue Oct 20 11:29:54 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 -parsing scores -* [Tue Sep 16 02:57:07 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 || : +* [Tue Oct 20 11:29:58 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 || : null device 1 -* [Tue Sep 16 02:57:08 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 +* [Tue Oct 20 11:29:59 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 null device 1 -* [Tue Sep 16 02:57:09 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 || : +* [Tue Oct 20 11:30:00 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:57:10 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 || : +* [Tue Oct 20 11:30:01 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:57:10 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 +* [Tue Oct 20 11:30:02 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 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 @@ -8043,33 +8079,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Tue Sep 16 02:57:10 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/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 +* [Tue Oct 20 11:30:02 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/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 -* [Tue Sep 16 02:57:28 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 +* [Tue Oct 20 11:30:19 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 -parsing scores -* [Tue Sep 16 02:57:32 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 || : +* [Tue Oct 20 11:30:24 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 || : null device 1 -* [Tue Sep 16 02:57:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Oct 20 11:30:26 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 null device 1 -* [Tue Sep 16 02:57:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Oct 20 11:30:28 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:57:35 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 +* [Tue Oct 20 11:30:29 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 Refining start codon selections. -number of revised start positions: 1 -* [Tue Sep 16 02:57:35 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* [Tue Sep 16 02:57:35 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 +* [Tue Oct 20 11:30:29 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* [Tue Oct 20 11:30:29 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Tue Sep 16 02:57:35 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 +* [Tue Oct 20 11:30:30 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Tue Sep 16 02:57:36 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 +* [Tue Oct 20 11:30:30 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 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.* @@ -8161,7 +8197,7 @@ ../../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 -* [Tue Sep 16 02:57:36 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 +* [Tue Oct 20 11:30:31 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 -first extracting base frequencies, we'll need them later. @@ -8185,8 +8221,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Tue Sep 16 02:57:38 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 -* [Tue Sep 16 02:57:38 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 +* [Tue Oct 20 11:30:34 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 +* [Tue Oct 20 11:30:34 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 -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 @@ -8861,37 +8897,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Tue Sep 16 02:57:39 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 +* [Tue Oct 20 11:30:35 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 PCT_GC: 42 -* [Tue Sep 16 02:57:39 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 -* [Tue Sep 16 02:57:40 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 -* [Tue Sep 16 02:57:45 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 +* [Tue Oct 20 11:30:35 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 +* [Tue Oct 20 11:30:36 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 +* [Tue Oct 20 11:30:43 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 Selecting best orfs -* [Tue Sep 16 02:57:46 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* [Tue Sep 16 02:57:46 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 -* [Tue Sep 16 02:57:46 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 +* [Tue Oct 20 11:30:43 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* [Tue Oct 20 11:30:43 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 +* [Tue Oct 20 11:30:44 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 02:58:14 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 +* [Tue Oct 20 11:31:33 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 -parsing scores -* [Tue Sep 16 02:58:22 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 || : +* [Tue Oct 20 11:31:41 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 || : null device 1 -* [Tue Sep 16 02:58:23 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 +* [Tue Oct 20 11:31:43 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 null device 1 -* [Tue Sep 16 02:58:25 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 || : +* [Tue Oct 20 11:31:45 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:58:25 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 || : +* [Tue Oct 20 11:31:46 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:58:26 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 +* [Tue Oct 20 11:31:47 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 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 @@ -8950,33 +8986,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Tue Sep 16 02:58:26 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 +* [Tue Oct 20 11:31:47 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 02:58:53 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 +* [Tue Oct 20 11:32:27 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.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 -* [Tue Sep 16 02:59:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Oct 20 11:32:34 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 || : null device 1 -* [Tue Sep 16 02:59:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Oct 20 11:32:35 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 null device 1 -* [Tue Sep 16 02:59:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Oct 20 11:32:37 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 02:59:03 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 +* [Tue Oct 20 11:32:37 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 Refining start codon selections. -number of revised start positions: 83 -* [Tue Sep 16 02:59:03 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* [Tue Sep 16 02:59:03 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/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 +* [Tue Oct 20 11:32:38 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* [Tue Oct 20 11:32:38 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Tue Sep 16 02:59:03 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/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 +* [Tue Oct 20 11:32:38 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Tue Sep 16 02:59:03 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/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 +* [Tue Oct 20 11:32:38 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 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.* @@ -9069,7 +9105,7 @@ 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 -* [Tue Sep 16 02:59:04 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 +* [Tue Oct 20 11:32:39 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 -first extracting base frequencies, we'll need them later. @@ -9089,8 +9125,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Tue Sep 16 02:59:07 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 -* [Tue Sep 16 02:59:07 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 +* [Tue Oct 20 11:32:41 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 +* [Tue Oct 20 11:32:42 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 -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 @@ -9128,37 +9164,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Tue Sep 16 02:59:07 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 +* [Tue Oct 20 11:32:42 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 PCT_GC: 38 -* [Tue Sep 16 02:59:07 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 -* [Tue Sep 16 02:59:09 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 -* [Tue Sep 16 02:59:15 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 +* [Tue Oct 20 11:32:43 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 +* [Tue Oct 20 11:32:44 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 +* [Tue Oct 20 11:32:50 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 Selecting best orfs -* [Tue Sep 16 02:59:15 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* [Tue Sep 16 02:59:15 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 -* [Tue Sep 16 02:59:15 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 +* [Tue Oct 20 11:32:50 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* [Tue Oct 20 11:32:50 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 +* [Tue Oct 20 11:32:51 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 02:59:50 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 +* [Tue Oct 20 11:33:25 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 -parsing scores -* [Tue Sep 16 02:59:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Oct 20 11:33:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Tue Sep 16 02:59:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Oct 20 11:33:33 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Tue Sep 16 03:00:01 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 || : +* [Tue Oct 20 11:33:35 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Tue Sep 16 03:00:02 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.-.pwm || : +* [Tue Oct 20 11:33:35 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Tue Sep 16 03:00:03 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 +* [Tue Oct 20 11:33:36 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 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 @@ -9264,33 +9300,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Tue Sep 16 03:00:04 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 +* [Tue Oct 20 11:33:36 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/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 -* [Tue Sep 16 03:00:41 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/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 +* [Tue Oct 20 11:34:03 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 -parsing scores -* [Tue Sep 16 03:00:47 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 || : +* [Tue Oct 20 11:34:10 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 || : null device 1 -* [Tue Sep 16 03:00:48 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 +* [Tue Oct 20 11:34:11 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 null device 1 -* [Tue Sep 16 03:00:49 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 || : +* [Tue Oct 20 11:34:12 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:00:50 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 +* [Tue Oct 20 11:34:13 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 Refining start codon selections. -number of revised start positions: 43 -* [Tue Sep 16 03:00:50 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* [Tue Sep 16 03:00:50 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 +* [Tue Oct 20 11:34:13 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* [Tue Oct 20 11:34:13 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Tue Sep 16 03:00:50 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/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 +* [Tue Oct 20 11:34:13 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Tue Sep 16 03:00:51 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 +* [Tue Oct 20 11:34:14 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 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.* @@ -9307,6 +9343,7 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', 'trans_id' => '', 'coords' => [ [ @@ -9315,24 +9352,23 @@ ] ], 'asmbl' => 'comp1051_c1_seq1', - 'orient' => '-', 'contig' => 'III', - 'gene_id' => '' + 'orient' => '-' }; - is_3prime_partial: 0 + classification: annotated_genes + gene_type: protein-coding + asmbl_id: comp1051_c1_seq1 strand: + + gene_length: 1616 TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 is_pseudogene: 0 - gene_type: protein-coding - gene_length: 1616 - com_name: ORF type:5prime_partial (+),score=83.26 - asmbl_id: comp1051_c1_seq1 - source: transdecoder - classification: annotated_genes + is_3prime_partial: 0 is_5prime_partial: 0 + Model_feat_name: comp1051_c1_seq1.p1 mid_pt: 808 + com_name: ORF type:5prime_partial (+),score=83.26 + source: transdecoder num_exons: 1 - Model_feat_name: comp1051_c1_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9349,10 +9385,9 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'contig' => 'I', + 'asmbl' => 'comp1058_c0_seq1', 'orient' => '-', - 'trans_id' => '', 'coords' => [ [ 5095548, @@ -9363,22 +9398,23 @@ '5095301' ] ], - 'asmbl' => 'comp1058_c0_seq1' + 'gene_id' => '', + 'trans_id' => '' }; - classification: annotated_genes - Model_feat_name: comp1058_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=32.57 + source: transdecoder num_exons: 1 - is_5prime_partial: 0 mid_pt: 248 - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - strand: + - is_3prime_partial: 0 + classification: annotated_genes + gene_type: protein-coding + Model_feat_name: comp1058_c0_seq1.p1 asmbl_id: comp1058_c0_seq1 - source: transdecoder + strand: + + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 gene_length: 496 - com_name: ORF type:5prime_partial (+),score=32.57 + is_3prime_partial: 0 + is_5prime_partial: 0 is_pseudogene: 0 - gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9401,8 +9437,6 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', - 'gene_id' => '', 'coords' => [ [ 2380416, @@ -9413,24 +9447,26 @@ '2380336' ] ], + 'orient' => '-', 'asmbl' => 'comp1112_c0_seq1', + 'contig' => 'III', 'trans_id' => '', - 'orient' => '-' + 'gene_id' => '' }; - Model_feat_name: comp1112_c0_seq1.p1 num_exons: 1 - is_5prime_partial: 0 - mid_pt: 1041 - classification: annotated_genes - asmbl_id: comp1112_c0_seq1 source: transdecoder - gene_length: 2081 com_name: ORF type:complete (+),score=155.28 - gene_type: protein-coding + mid_pt: 1041 + Model_feat_name: comp1112_c0_seq1.p1 + is_5prime_partial: 0 + is_3prime_partial: 0 is_pseudogene: 0 TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + gene_length: 2081 strand: + - is_3prime_partial: 0 + asmbl_id: comp1112_c0_seq1 + gene_type: protein-coding + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9452,11 +9488,9 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'contig' => 'II', - 'orient' => '-', - 'trans_id' => '', 'asmbl' => 'comp1198_c0_seq1', + 'orient' => '-', 'coords' => [ [ 402195, @@ -9474,22 +9508,24 @@ 401352, '401683' ] - ] + ], + 'gene_id' => '', + 'trans_id' => '' }; - is_5prime_partial: 0 mid_pt: 299 num_exons: 1 - Model_feat_name: comp1198_c0_seq1.p1 - classification: annotated_genes - is_pseudogene: 0 - gene_type: protein-coding - gene_length: 597 com_name: ORF type:internal (+),score=37.56 - asmbl_id: comp1198_c0_seq1 source: transdecoder + gene_type: protein-coding + classification: annotated_genes + gene_length: 597 + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + is_pseudogene: 0 + is_5prime_partial: 0 is_3prime_partial: 0 + asmbl_id: comp1198_c0_seq1 strand: + - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + Model_feat_name: comp1198_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9518,8 +9554,8 @@ Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'contig' => 'III', - 'gene_id' => '', 'asmbl' => 'comp1210_c0_seq1', + 'orient' => '-', 'coords' => [ [ 368840, @@ -9530,23 +9566,23 @@ '368790' ] ], - 'trans_id' => '', - 'orient' => '-' + 'gene_id' => '', + 'trans_id' => '' }; - classification: annotated_genes - is_5prime_partial: 0 - mid_pt: 777 - Model_feat_name: comp1210_c0_seq1.p1 num_exons: 1 - strand: + - is_3prime_partial: 0 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 - gene_length: 1554 com_name: ORF type:5prime_partial (+),score=12.16 + source: transdecoder + mid_pt: 777 gene_type: protein-coding + classification: annotated_genes + Model_feat_name: comp1210_c0_seq1.p1 + gene_length: 1554 + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 is_pseudogene: 0 + is_5prime_partial: 0 + is_3prime_partial: 0 asmbl_id: comp1210_c0_seq1 - source: transdecoder + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9571,32 +9607,32 @@ -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 = { - 'gene_id' => '', - 'contig' => 'II', - 'orient' => '-', 'coords' => [ [ '3840968', '3841303' ] ], + 'orient' => '-', 'asmbl' => 'comp366_c0_seq1', - 'trans_id' => '' + 'contig' => 'II', + 'trans_id' => '', + 'gene_id' => '' }; + gene_type: protein-coding + classification: annotated_genes + Model_feat_name: comp366_c0_seq1.p1 + gene_length: 340 TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + is_pseudogene: 0 + is_5prime_partial: 0 is_3prime_partial: 0 - strand: - - source: transdecoder asmbl_id: comp366_c0_seq1 - is_pseudogene: 0 - gene_type: protein-coding - com_name: ORF type:internal (-),score=12.83 - gene_length: 340 - classification: annotated_genes + strand: - num_exons: 1 - Model_feat_name: comp366_c0_seq1.p1 + com_name: ORF type:internal (-),score=12.83 + source: transdecoder mid_pt: 170 - is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9622,31 +9658,31 @@ -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 = { + 'trans_id' => '', 'gene_id' => '', - 'contig' => 'I', - 'orient' => '-', 'coords' => [ [ '5471264', '5472770' ] ], - 'asmbl' => 'comp610_c0_seq1', - 'trans_id' => '' + 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp610_c0_seq1' }; - classification: annotated_genes - Model_feat_name: comp610_c0_seq1.p1 + source: transdecoder + com_name: ORF type:5prime_partial (+),score=50.55 num_exons: 1 - is_5prime_partial: 0 mid_pt: 755 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + Model_feat_name: comp610_c0_seq1.p1 strand: + - is_3prime_partial: 0 asmbl_id: comp610_c0_seq1 - source: transdecoder - gene_length: 1509 - com_name: ORF type:5prime_partial (+),score=50.55 is_pseudogene: 0 + is_5prime_partial: 0 + is_3prime_partial: 0 + gene_length: 1509 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + classification: annotated_genes gene_type: protein-coding gene_synonyms: mRNA_coords @@ -9666,32 +9702,32 @@ -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 = { - 'gene_id' => '', - 'contig' => 'I', - 'orient' => '-', - 'asmbl' => 'comp645_c0_seq1', 'coords' => [ [ '4333088', '4336727' ] ], - 'trans_id' => '' + 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp645_c0_seq1', + 'trans_id' => '', + 'gene_id' => '' }; - is_5prime_partial: 0 mid_pt: 1827 - Model_feat_name: comp645_c0_seq1.p1 num_exons: 1 - classification: annotated_genes - gene_length: 3653 com_name: ORF type:5prime_partial (+),score=273.35 - gene_type: protein-coding + source: transdecoder + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + gene_length: 3653 + is_3prime_partial: 0 + is_5prime_partial: 0 is_pseudogene: 0 asmbl_id: comp645_c0_seq1 - source: transdecoder strand: + - is_3prime_partial: 0 - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + Model_feat_name: comp645_c0_seq1.p1 + gene_type: protein-coding + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9707,9 +9743,8 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', - 'gene_id' => '', 'trans_id' => '', + 'gene_id' => '', 'coords' => [ [ 380308, @@ -9720,23 +9755,24 @@ '381243' ] ], + 'orient' => '+', 'asmbl' => 'comp688_c0_seq1', - 'orient' => '+' + 'contig' => 'II' }; - Model_feat_name: comp688_c0_seq1.p1 - num_exons: 1 mid_pt: 1392 - is_5prime_partial: 0 - classification: annotated_genes - source: transdecoder - asmbl_id: comp688_c0_seq1 + num_exons: 1 com_name: ORF type:complete (+),score=172.54 - gene_length: 2784 - is_pseudogene: 0 + source: transdecoder gene_type: protein-coding + classification: annotated_genes + gene_length: 2784 TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 - strand: + + is_pseudogene: 0 is_3prime_partial: 0 + is_5prime_partial: 0 + asmbl_id: comp688_c0_seq1 + strand: + + Model_feat_name: comp688_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9760,11 +9796,8 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'contig' => 'II', - 'orient' => '+', 'trans_id' => '', - 'asmbl' => 'comp856_c0_seq1', + 'gene_id' => '', 'coords' => [ [ 3753910, @@ -9774,22 +9807,25 @@ 3754438, '3755057' ] - ] + ], + 'orient' => '+', + 'asmbl' => 'comp856_c0_seq1', + 'contig' => 'II' }; - is_5prime_partial: 0 mid_pt: 785 num_exons: 1 - Model_feat_name: comp856_c0_seq1.p1 - classification: annotated_genes - gene_type: protein-coding - is_pseudogene: 0 - gene_length: 1569 - com_name: ORF type:complete (+),score=71.94 - asmbl_id: comp856_c0_seq1 source: transdecoder + com_name: ORF type:complete (+),score=71.94 + is_5prime_partial: 0 is_3prime_partial: 0 - strand: + + is_pseudogene: 0 TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + gene_length: 1569 + strand: + + asmbl_id: comp856_c0_seq1 + Model_feat_name: comp856_c0_seq1.p1 + gene_type: protein-coding + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9809,10 +9845,9 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'contig' => 'II', - 'orient' => '-', 'asmbl' => 'comp873_c0_seq2', + 'orient' => '-', 'coords' => [ [ 3727877, @@ -9827,22 +9862,23 @@ '3727657' ] ], + 'gene_id' => '', 'trans_id' => '' }; classification: annotated_genes - Model_feat_name: comp873_c0_seq2.p1 - num_exons: 1 - is_5prime_partial: 0 - mid_pt: 513 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 - strand: + - is_3prime_partial: 0 + gene_type: protein-coding asmbl_id: comp873_c0_seq2 - source: transdecoder + strand: + gene_length: 1025 - com_name: ORF type:5prime_partial (+),score=8.59 + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 is_pseudogene: 0 - gene_type: protein-coding + is_5prime_partial: 0 + is_3prime_partial: 0 + Model_feat_name: comp873_c0_seq2.p1 + mid_pt: 513 + com_name: ORF type:5prime_partial (+),score=8.59 + source: transdecoder + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9867,8 +9903,6 @@ Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', - 'contig' => 'III', - 'orient' => '-', 'trans_id' => '', 'coords' => [ [ @@ -9880,22 +9914,24 @@ '1268172' ] ], - 'asmbl' => 'comp888_c0_seq1' + 'asmbl' => 'comp888_c0_seq1', + 'contig' => 'III', + 'orient' => '-' }; mid_pt: 295 - is_5prime_partial: 0 - Model_feat_name: comp888_c0_seq1.p1 num_exons: 1 - classification: annotated_genes com_name: ORF type:5prime_partial (+),score=23.94 + source: transdecoder + gene_type: protein-coding + classification: annotated_genes + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_length: 589 + is_3prime_partial: 0 + is_5prime_partial: 0 is_pseudogene: 0 - gene_type: protein-coding - source: transdecoder asmbl_id: comp888_c0_seq1 strand: + - is_3prime_partial: 0 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 + Model_feat_name: comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9918,7 +9954,9 @@ Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', + 'trans_id' => '', 'contig' => 'III', + 'asmbl' => 'comp940_c0_seq1', 'orient' => '+', 'coords' => [ [ @@ -9929,24 +9967,22 @@ 105785, '106404' ] - ], - 'asmbl' => 'comp940_c0_seq1', - 'trans_id' => '' + ] }; + mid_pt: 1065 + num_exons: 1 + com_name: ORF type:complete (+),score=94.37 + source: transdecoder TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + gene_length: 2129 + is_5prime_partial: 0 is_3prime_partial: 0 - strand: + - asmbl_id: comp940_c0_seq1 - source: transdecoder is_pseudogene: 0 + asmbl_id: comp940_c0_seq1 + strand: + + Model_feat_name: comp940_c0_seq1.p1 gene_type: protein-coding - gene_length: 2129 - com_name: ORF type:complete (+),score=94.37 classification: annotated_genes - num_exons: 1 - Model_feat_name: comp940_c0_seq1.p1 - is_5prime_partial: 0 - mid_pt: 1065 gene_synonyms: mRNA_coords CDS_coords @@ -9966,8 +10002,8 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', 'trans_id' => '', + 'gene_id' => '', 'coords' => [ [ 4100066, @@ -9978,24 +10014,24 @@ '4100014' ] ], + 'orient' => '-', 'asmbl' => 'comp983_c0_seq1', - 'gene_id' => '', 'contig' => 'I' }; + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + gene_length: 1870 + is_3prime_partial: 0 is_5prime_partial: 0 - mid_pt: 935 + is_pseudogene: 0 + asmbl_id: comp983_c0_seq1 + strand: + Model_feat_name: comp983_c0_seq1.p1 - num_exons: 1 + gene_type: protein-coding classification: annotated_genes - gene_length: 1870 + mid_pt: 935 + num_exons: 1 com_name: ORF type:5prime_partial (+),score=143.65 - is_pseudogene: 0 - gene_type: protein-coding - asmbl_id: comp983_c0_seq1 source: transdecoder - strand: + - is_3prime_partial: 0 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -10039,7 +10075,7 @@ ## 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 -* [Tue Sep 16 03:00:53 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 +* [Tue Oct 20 11:34:16 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 -first extracting base frequencies, we'll need them later. @@ -10064,8 +10100,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Tue Sep 16 03:01:05 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 -* [Tue Sep 16 03:01:06 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 +* [Tue Oct 20 11:34:28 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 +* [Tue Oct 20 11:34:29 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 -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 @@ -12683,37 +12719,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Tue Sep 16 03:01:08 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 +* [Tue Oct 20 11:34:31 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 PCT_GC: 46 -* [Tue Sep 16 03:01:08 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 -* [Tue Sep 16 03:01:11 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 -* [Tue Sep 16 03:01:43 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 +* [Tue Oct 20 11:34:31 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 +* [Tue Oct 20 11:34:34 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 +* [Tue Oct 20 11:35:06 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 Selecting best orfs -* [Tue Sep 16 03:01:44 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* [Tue Sep 16 03:01:44 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 -* [Tue Sep 16 03:01:45 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 +* [Tue Oct 20 11:35:07 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* [Tue Oct 20 11:35:07 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 +* [Tue Oct 20 11:35:09 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 03:02:15 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 +* [Tue Oct 20 11:35:41 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 -parsing scores -* [Tue Sep 16 03:02:23 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 || : +* [Tue Oct 20 11:35:49 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 || : null device 1 -* [Tue Sep 16 03:02:24 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 +* [Tue Oct 20 11:35:50 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 null device 1 -* [Tue Sep 16 03:02:25 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 || : +* [Tue Oct 20 11:35:51 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:02:26 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 || : +* [Tue Oct 20 11:35:52 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:02:26 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 +* [Tue Oct 20 11:35:53 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 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 @@ -12816,33 +12852,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Tue Sep 16 03:02:27 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 +* [Tue Oct 20 11:35:53 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 03:02:55 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 +* [Tue Oct 20 11:36:21 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 -parsing scores -* [Tue Sep 16 03:03:01 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 || : +* [Tue Oct 20 11:36:28 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 || : null device 1 -* [Tue Sep 16 03:03:03 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 +* [Tue Oct 20 11:36:29 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 null device 1 -* [Tue Sep 16 03:03:04 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 || : +* [Tue Oct 20 11:36:30 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:03:05 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 +* [Tue Oct 20 11:36:31 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 Refining start codon selections. -number of revised start positions: 247 -* [Tue Sep 16 03:03:06 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* [Tue Sep 16 03:03:06 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 +* [Tue Oct 20 11:36:32 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* [Tue Oct 20 11:36:32 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Tue Sep 16 03:03:07 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 +* [Tue Oct 20 11:36:32 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Tue Sep 16 03:03:08 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 +* [Tue Oct 20 11:36:34 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 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.* @@ -12954,7 +12990,7 @@ // 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 -* [Tue Sep 16 03:03:17 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 +* [Tue Oct 20 11:36:42 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 -first extracting base frequencies, we'll need them later. @@ -12978,19 +13014,19 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Tue Sep 16 03:03:19 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 -* [Tue Sep 16 03:03:19 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 +* [Tue Oct 20 11:36:43 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 +* [Tue Oct 20 11:36:43 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 -skipping training candidate: bdg_i3.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_i2.p1, not unique enough -skipping training candidate: eIF5B_i4.p1, not unique enough +-skipping training candidate: eIF5B_i3.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_i3.p1, not unique enough -skipping training candidate: Dgk_i6.p1, not unique enough +-skipping training candidate: Dgk_i3.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough @@ -13000,32 +13036,32 @@ -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_i5.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_i1.p1, not unique enough +-skipping training candidate: Calx_i5.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_i6.p1, not unique enough -skipping training candidate: Klp10A_i2.p1, not unique enough -skipping training candidate: Klp10A_i1.p1, not unique enough --skipping training candidate: Klp10A_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: CG6424_i3.p1, not unique enough +-skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough +-skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough --skipping training candidate: CG33970_i2.p1, not unique enough +-skipping training candidate: CG33970_i1.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough --skipping training candidate: CG12581_i2.p1, not unique enough --skipping training candidate: CG6091_i1.p1, not unique enough --skipping training candidate: hrg_i4.p1, not unique enough --skipping training candidate: hrg_i2.p1, not unique enough +-skipping training candidate: CG12581_i1.p1, not unique enough +-skipping training candidate: CG6091_i3.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough +-skipping training candidate: hrg_i2.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 @@ -13034,8 +13070,8 @@ -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough -skipping training candidate: l(3)05822_i3.p1, not unique enough --skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i3.p1, not unique enough +-skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough -skipping training candidate: l(3)05822_i1.p1, not unique enough @@ -13046,631 +13082,628 @@ -skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough --skipping training candidate: Est-6_i1.p1, not unique enough +-skipping training candidate: Est-6_i2.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: S-Lap3_i1.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_i3.p1, not unique enough +-skipping training candidate: CG30438_i1.p1, not unique enough -skipping training candidate: CG30438_i5.p1, not unique enough --skipping training candidate: CG30438_i2.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_i3.p1, not unique enough +-skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i1.p1, not unique enough --skipping training candidate: Eno_i5.p1, not unique enough +-skipping training candidate: Eno_i3.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough -skipping training candidate: Aldh-III_i4.p1, not unique enough --skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i3.p1, not unique enough --skipping training candidate: Aldh-III_i8.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough --skipping training candidate: Galk_i1.p1, not unique enough --skipping training candidate: Galk_i3.p1, not unique enough +-skipping training candidate: Aldh-III_i8.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_i5.p2, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough --skipping training candidate: Eno_i3.p2, not unique enough -skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: Eno_i5.p2, not unique enough +-skipping training candidate: Eno_i3.p2, not unique enough -skipping training candidate: Eno_i6.p1, 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_i1.p2, not unique enough +-skipping training candidate: CG6424_i3.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 --skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Irk2_i4.p1, not unique enough +-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_i2.p1, not unique enough --skipping training candidate: AdipoR_i4.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_i4.p1, not unique enough +-skipping training candidate: AdipoR_i2.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_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_i1.p1, not unique enough +-skipping training candidate: nmo_i1.p1, not unique enough +-skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough --skipping training candidate: CG7564_i2.p3, not unique enough --skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG7564_i3.p1, not unique enough +-skipping training candidate: CG7564_i4.p1, not unique enough +-skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG14995_i7.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: nmo_i5.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 --skipping training candidate: CG6024_i2.p1, not unique enough +-skipping training candidate: CG6024_i1.p1, not unique enough -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_i5.p1, not unique enough --skipping training candidate: ogre_i3.p1, not unique enough --skipping training candidate: ogre_i2.p1, not unique enough -skipping training candidate: ogre_i6.p1, not unique enough -skipping training candidate: ogre_i1.p1, not unique enough +-skipping training candidate: ogre_i5.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: 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_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_i6.p2, not unique enough -skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Klp10A_i1.p2, not unique enough --skipping training candidate: Klp10A_i4.p2, 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: 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_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_i1.p1, not unique enough --skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i4.p1, not unique enough --skipping training candidate: CG10237_i3.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: l(3)05822_i3.p2, not unique enough +-skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: l(3)05822_i2.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: Tm1_i9.p1, not unique enough --skipping training candidate: Tm1_i2.p1, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Tm1_i9.p1, not unique enough +-skipping training candidate: Tm1_i11.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: Npl4_i1.p2, not unique enough -skipping training candidate: Npl4_i2.p2, not unique enough -skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i2.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_i7.p2, not unique enough --skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: CG8312_i4.p2, not unique enough +-skipping training candidate: Dgk_i1.p2, not unique enough +-skipping training candidate: eIF5B_i1.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: eIF5B_i1.p2, not unique enough --skipping training candidate: Dgk_i3.p2, not unique enough --skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: eIF5B_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: l(1)G0193_i1.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: l(1)G0193_i2.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough --skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough +-skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough --skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough --skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough --skipping training candidate: l(3)05822_i3.p3, not unique enough +-skipping training candidate: Dgk_i6.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: l(3)05822_i2.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: CG14995_i5.p1, not unique enough --skipping training candidate: CG6024_i2.p2, not unique enough +-skipping training candidate: CG6024_i1.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: CG13887_i2.p1, not unique enough -skipping training candidate: CG13887_i4.p1, not unique enough --skipping training candidate: CG13887_i1.p1, not unique enough --skipping training candidate: CG14995_i7.p2, not unique enough +-skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough --skipping training candidate: nmo_i5.p2, not unique enough --skipping training candidate: nmo_i7.p2, not unique enough -skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i1.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_i3.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough +-skipping training candidate: nmo_i5.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_i4.p3, not unique enough -skipping training candidate: gukh_i3.p2, not unique enough +-skipping training candidate: gukh_i4.p3, 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_i2.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough +-skipping training candidate: RpL15_i1.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough --skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: Npl4_i2.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: trc_i1.p2, 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_i1.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG10237_i5.p2, not unique enough +-skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough -skipping training candidate: CG10237_i4.p2, not unique enough --skipping training candidate: Eno_i3.p3, not unique enough +-skipping training candidate: Eno_i4.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Eno_i1.p3, not unique enough --skipping training candidate: Eno_i5.p3, not unique enough +-skipping training candidate: Eno_i3.p3, not unique enough -skipping training candidate: Eno_i6.p3, not unique enough --skipping training candidate: Eno_i2.p3, not unique enough +-skipping training candidate: Sec16_i1.p3, not unique enough -skipping training candidate: Sec16_i3.p2, 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: CG14995_i3.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: gukh_i1.p3, 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: CG10082_i1.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough --skipping training candidate: CG30438_i1.p2, not unique enough +-skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG30438_i3.p2, not unique enough +-skipping training candidate: CG30438_i4.p2, not unique enough +-skipping training candidate: CG30438_i1.p2, not unique enough -skipping training candidate: CG30438_i5.p2, not unique enough --skipping training candidate: CG30438_i2.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_i1.p3, not unique enough +-skipping training candidate: cdi_i2.p2, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CanB2_i1.p1, not unique enough --skipping training candidate: ADD1_i2.p2, not unique enough +-skipping training candidate: CanB2_i2.p1, not unique enough +-skipping training candidate: ADD1_i3.p2, not unique enough +-skipping training candidate: Sec16_i1.p4, not unique enough -skipping training candidate: Sec16_i3.p3, 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: bic_i2.p1, not unique enough +-skipping training candidate: CG12581_i1.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i2.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_i3.p2, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough --skipping training candidate: Eno_i3.p4, not unique enough +-skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Eno_i1.p4, not unique enough --skipping training candidate: Eno_i5.p4, not unique enough +-skipping training candidate: Eno_i3.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Eno_i2.p4, not unique enough +-skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i2.p4, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough --skipping training candidate: Klp10A_i4.p3, not unique enough -skipping training candidate: Klp10A_i5.p3, not unique enough --skipping training candidate: Klp10A_i6.p3, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i5.p2, not unique enough --skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Klp10A_i3.p3, not unique enough +-skipping training candidate: Calx_i2.p2, not unique enough -skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i6.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_i8.p2, not unique enough +-skipping training candidate: Calx_i3.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough --skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: CG7564_i1.p2, 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: CG7564_i3.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: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i1.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: eIF5B_i1.p3, not unique enough +-skipping training candidate: eIF5B_i3.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: AdipoR_i4.p2, not unique enough -skipping training candidate: CG6424_i2.p3, 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_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_i5.p2, not unique enough -skipping training candidate: Tm1_i14.p2, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Tm1_i5.p2, 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_i7.p5, not unique enough --skipping training candidate: cdi_i1.p4, not unique enough --skipping training candidate: eff_i2.p1, not unique enough +-skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Dgk_i3.p4, 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_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i2.p4, not unique enough +-skipping training candidate: eIF5B_i1.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: eIF5B_i1.p4, not unique enough --skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: eIF5B_i3.p4, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough --skipping training candidate: Sec16_i4.p5, not unique enough +-skipping training candidate: Sec16_i3.p4, 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_i2.p2, not unique enough -skipping training candidate: CG32082_i1.p2, not unique enough --skipping training candidate: CG32082_i3.p2, not unique enough --skipping training candidate: CG3530_i1.p2, not unique enough +-skipping training candidate: CG3530_i3.p2, not unique enough -skipping training candidate: CG3530_i2.p2, not unique enough --skipping training candidate: Dgk_i7.p6, not unique enough --skipping training candidate: l(3)05822_i3.p4, not unique enough +-skipping training candidate: Dgk_i2.p6, not unique enough -skipping training candidate: l(3)05822_i2.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: sqd_i1.p2, not unique enough --skipping training candidate: CG7564_i2.p6, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: CG7564_i3.p4, not unique enough +-skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: CG7564_i2.p6, 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: S-Lap3_i1.p2, not unique enough --skipping training candidate: cdi_i1.p5, not unique enough --skipping training candidate: CG6091_i3.p2, not unique enough --skipping training candidate: CG6091_i1.p2, not unique enough +-skipping training candidate: cdi_i2.p4, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough --skipping training candidate: Cdep_i3.p2, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough +-skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough --skipping training candidate: Cnx99A_i2.p2, not unique enough --skipping training candidate: Cnx99A_i4.p2, not unique enough +-skipping training candidate: Cdep_i3.p2, not unique enough -skipping training candidate: Cnx99A_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: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i3.p5, not unique enough --skipping training candidate: Sec16_i6.p4, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough --skipping training candidate: ogre_i6.p2, not unique enough --skipping training candidate: CG6024_i2.p3, not unique enough --skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: ogre_i3.p2, not unique enough +-skipping training candidate: CG6024_i1.p3, not unique enough -skipping training candidate: hrg_i1.p3, not unique enough +-skipping training candidate: hrg_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i3.p2, not unique enough --skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: CG6091_i1.p3, not unique enough +-skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough +-skipping training candidate: CG33970_i3.p2, not unique enough -skipping training candidate: CG33970_i1.p2, not unique enough --skipping training candidate: CG33970_i2.p2, not unique enough --skipping training candidate: eIF5B_i3.p5, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough --skipping training candidate: Aldh-III_i11.p2, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i5.p2, not unique enough --skipping training candidate: CG13284_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i8.p2, not unique enough -skipping training candidate: CG13284_i1.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough --skipping training candidate: Lip4_i2.p2, not unique enough +-skipping training candidate: CG13284_i4.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: Dgk_i7.p7, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough --skipping training candidate: Dgk_i6.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_i1.p5, not unique enough --skipping training candidate: Dgk_i7.p7, not unique enough +-skipping training candidate: Dgk_i6.p5, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Tm1_i16.p3, not unique enough --skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: Tm1_i14.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: CG8312_i1.p2, not unique enough -skipping training candidate: CG8312_i1.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_i4.p3, not unique enough +-skipping training candidate: CG8312_i4.p4, not unique enough +-skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i2.p6, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough --skipping training candidate: Klp10A_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: eff_i2.p2, not unique enough +-skipping training candidate: Klp10A_i3.p4, not unique enough +-skipping training candidate: eff_i1.p2, not unique enough -skipping training candidate: eff_i3.p2, not unique enough --skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough +-skipping training candidate: CG14995_i5.p5, not unique enough +-skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i4.p4, not unique enough --skipping training candidate: CG6424_i4.p4, not unique enough -skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough --skipping training candidate: CG12581_i2.p3, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough +-skipping training candidate: CG12581_i1.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough -skipping training candidate: CG32082_i1.p3, not unique enough --skipping training candidate: CG32082_i3.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: Cnx99A_i2.p3, not unique enough +-skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Cdep_i4.p2, not unique enough --skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough +-skipping training candidate: CG33970_i3.p3, not unique enough -skipping training candidate: CG33970_i1.p3, not unique enough --skipping training candidate: CG33970_i2.p3, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: Sec16_i4.p7, not unique enough -skipping training candidate: Sec16_i6.p5, not unique enough +-skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: Sec16_i2.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_i3.p6, not unique enough -skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough --skipping training candidate: CG6024_i2.p4, not unique enough +-skipping training candidate: CG6024_i1.p4, not unique enough +-skipping training candidate: Myo61F_i1.p2, 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_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i2.p4, not unique enough -skipping training candidate: Cnx99A_i3.p4, not unique enough +-skipping training candidate: Cnx99A_i2.p4, not unique enough +-skipping training candidate: CG13887_i2.p2, not unique enough -skipping training candidate: CG13887_i4.p2, not unique enough --skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG6145_i3.p2, 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_i3.p2, not unique enough +-skipping training candidate: CG6145_i4.p2, not unique enough -skipping training candidate: CG6145_i2.p2, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i5.p3, not unique enough --skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: Calx_i2.p3, not unique enough -skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i6.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_i8.p3, not unique enough +-skipping training candidate: Calx_i3.p3, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough --skipping training candidate: Calx_i9.p3, 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_i4.p3, not unique enough +-skipping training candidate: mge_i2.p2, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i3.p3, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough +-skipping training candidate: AdipoR_i2.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_i1.p2, not unique enough --skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Aldh-III_i6.p2, not unique enough +-skipping training candidate: Aldh-III_i1.p2, not unique enough -skipping training candidate: Aldh-III_i10.p3, not unique enough --skipping training candidate: Cdep_i4.p3, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough +-skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Cdep_i2.p9, not unique enough --skipping training candidate: Cdep_i1.p4, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough --skipping training candidate: hrg_i2.p2, 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_i2.p2, not unique enough +-skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: CG33125_i2.p2, 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: CG12581_i1.p4, not unique enough -skipping training candidate: Sec16_i6.p6, not unique enough -skipping training candidate: Sec16_i6.p7, 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_i2.p8, not unique enough -skipping training candidate: Sec16_i2.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_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: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough --skipping training candidate: CG6091_i3.p4, not unique enough --skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough --skipping training candidate: CanB2_i1.p2, not unique enough --skipping training candidate: IP3K1_i1.p3, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough +-skipping training candidate: CG6091_i3.p4, not unique enough +-skipping training candidate: CanB2_i2.p2, not unique enough +-skipping training candidate: IP3K1_i2.p2, not unique enough +-skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough --skipping training candidate: Klp10A_i4.p5, 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: AdipoR_i2.p3, not unique enough --skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Cdep_i2.p10, not unique enough --skipping training candidate: Cdep_i1.p5, not unique enough --skipping training candidate: Est-6_i1.p2, 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_i2.p2, not unique enough +-skipping training candidate: Klp10A_i6.p6, not unique enough -skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: Klp10A_i1.p7, not unique enough --skipping training candidate: Klp10A_i4.p6, 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: l(3)05822_i3.p5, not unique enough --skipping training candidate: ADD1_i2.p3, not unique enough +-skipping training candidate: ADD1_i3.p4, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i2.p5, not unique enough --skipping training candidate: Cnx99A_i4.p3, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough +-skipping training candidate: Cnx99A_i4.p3, 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.p3, not unique enough -skipping training candidate: Myo61F_i4.p3, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough +-skipping training candidate: Myo61F_i1.p4, 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.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: bic_i2.p2, not unique enough +-skipping training candidate: CG10082_i1.p5, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough -skipping training candidate: CG32082_i1.p4, not unique enough --skipping training candidate: CG32082_i3.p4, not unique enough --skipping training candidate: Eno_i3.p5, not unique enough +-skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Eno_i1.p6, not unique enough --skipping training candidate: Eno_i5.p6, not unique enough +-skipping training candidate: Eno_i3.p5, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough --skipping training candidate: Eno_i2.p5, not unique enough +-skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough --skipping training candidate: Sec16_i4.p10, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i6.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_i1.p6, not unique enough --skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Dgk_i6.p6, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: nmo_i4.p3, not unique enough --skipping training candidate: CG33970_i2.p5, 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_i1.p7, not unique enough --skipping training candidate: His4r_i2.p1, not unique enough +-skipping training candidate: Dgk_i3.p7, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough +-skipping training candidate: His4r_i2.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: hrg_i4.p6, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: hrg_i1.p5, not unique enough --skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: hrg_i4.p6, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough +-skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough +-skipping training candidate: Myo61F_i1.p5, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough -skipping training candidate: Myo61F_i4.p5, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough --skipping training candidate: CG6091_i3.p5, not unique enough --skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough --skipping training candidate: CG6145_i1.p3, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough +-skipping training candidate: CG6091_i3.p5, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough +-skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: CG6145_i2.p3, not unique enough --skipping training candidate: gukh_i2.p3, not unique enough +-skipping training candidate: gukh_i1.p4, not unique enough -skipping training candidate: sqd_i3.p3, not unique enough -skipping training candidate: CG33125_i2.p3, not unique enough --skipping training candidate: gukh_i2.p4, not unique enough +-skipping training candidate: gukh_i1.p5, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Tue Sep 16 03:03:19 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 +* [Tue Oct 20 11:36:44 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 PCT_GC: 49.4 -* [Tue Sep 16 03:03:19 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/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 -* [Tue Sep 16 03:03:20 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/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 -* [Tue Sep 16 03:03:25 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 +* [Tue Oct 20 11:36:44 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 +* [Tue Oct 20 11:36:44 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 +* [Tue Oct 20 11:36:50 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 Selecting best orfs -* [Tue Sep 16 03:03:25 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* [Tue Sep 16 03:03:26 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 -* [Tue Sep 16 03:03:26 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 +* [Tue Oct 20 11:36:50 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* [Tue Oct 20 11:36:50 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 +* [Tue Oct 20 11:36:50 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Tue Sep 16 03:03:54 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.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Oct 20 11:37:18 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 -parsing scores -* [Tue Sep 16 03:04:01 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 || : +* [Tue Oct 20 11:37:25 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 || : null device 1 -* [Tue Sep 16 03:04:02 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 +* [Tue Oct 20 11:37:26 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 null device 1 -* [Tue Sep 16 03:04:03 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 || : +* [Tue Oct 20 11:37:27 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:04:04 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 || : +* [Tue Oct 20 11:37:28 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:04:04 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 +* [Tue Oct 20 11:37:28 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 num features: 253 num_incorporate: 75 --feature swap of score: -1.39518097247344 instead of -3.64748011460695 --feature swap of score: -1.39925128017183 instead of -3.44677846967632 --feature swap of score: -1.67327206189302 instead of -2.96221872660412 --feature swap of score: -1.40456187614297 instead of -1.43355726710183 --feature swap of score: -0.536507663662479 instead of -1.00754582195429 --feature swap of score: 1.95518231907968 instead of -1.04741542168602 --feature swap of score: -0.488362584146478 instead of -0.954487504775416 --feature swap of score: 2.77849457514418 instead of -0.9268389779659 --feature swap of score: -0.578148538793991 instead of -1.0349694471474 --feature swap of score: 2.33579538643598 instead of -0.955771234422413 --feature swap of score: -0.316000035431064 instead of -0.82577359052634 --feature swap of score: 0.740381220549901 instead of -1.1456901101077 --feature swap of score: 1.70403137207803 instead of -1.12723414817074 --feature swap of score: 1.28756705464408 instead of -1.42122321751794 --feature swap of score: -0.691000556236704 instead of -0.983252909192325 --feature swap of score: -0.0944253904914663 instead of -0.896500080533309 --feature swap of score: -0.564661493746867 instead of -1.22475083592565 --feature swap of score: -0.412609812530464 instead of -0.499483713877633 --feature swap of score: 1.31497087751653 instead of -0.460431679635248 --feature swap of score: -1.73703356169764 instead of -1.90451262535291 --feature swap of score: 3.10600407275935 instead of -0.644260812723597 --feature swap of score: 1.88930028429158 instead of -0.516687284285068 --feature swap of score: 0.795374598071167 instead of -0.300851512765529 --feature swap of score: 2.75375965611415 instead of -0.318581558584142 --feature swap of score: 0.353439913732787 instead of -0.324802904717371 --feature swap of score: 2.34949374993722 instead of -0.735516178506623 --feature swap of score: 0.74156296954447 instead of -0.441907110420623 --feature swap of score: 1.4655252899487 instead of -0.426958636980015 --feature swap of score: 0.837621644078077 instead of -0.467280965062725 --feature swap of score: 3.13600230460039 instead of -0.585074029442215 --feature swap of score: 0.125374950379237 instead of -0.707677967899551 --feature swap of score: 0.926877534481064 instead of -0.865657959951598 --feature swap of score: 0.289750188721488 instead of -0.997433286885864 --feature swap of score: 1.39063959948275 instead of -1.29041803756393 --feature swap of score: 0.90287117416974 instead of -0.887863308804752 --feature swap of score: 0.113696148355266 instead of -0.536208914941287 --feature swap of score: 2.61413468504883 instead of -0.524688911044247 --feature swap of score: 0.694251556563588 instead of -0.774201157256379 --feature swap of score: 1.45238878345514 instead of -0.474221176228054 --feature swap of score: -0.111745841049778 instead of -0.782216444069408 --feature swap of score: 0.0536149412431958 instead of -0.380144533582495 --feature swap of score: 0.296073444180268 instead of 0.076165190890946 --feature swap of score: -0.0159101406883027 instead of -0.147194896250748 --feature swap of score: 0.873273158925026 instead of -0.226488007557527 --feature swap of score: 0.980871599342371 instead of -0.285393370439898 --feature swap of score: -0.0810970659424854 instead of -0.522097953784326 --feature swap of score: 0.385478872488974 instead of 0.252392595825185 --feature swap of score: 3.45367067149643 instead of 0.216900138651196 --feature swap of score: 1.07382132400491 instead of 0.0436348516004563 --feature swap of score: 1.12228826031283 instead of -0.010114455082215 --feature swap of score: 1.62158043660347 instead of 0.0853552378679648 --feature swap of score: 0.929202296488356 instead of 0.0730488090848406 --feature swap of score: 0.247708478493905 instead of 0.112258923591403 --feature swap of score: 0.691491488219101 instead of 0.0424207130320461 --feature swap of score: 7.56214267853945 instead of 0.306848634084634 --feature swap of score: 1.76668360156162 instead of 0.373602699692021 --feature swap of score: 8.6913082202093 instead of 0.240777626149078 --feature swap of score: 2.28568274908437 instead of 0.214935353450169 --num feature swaps: 58 -* [Tue Sep 16 03:04:05 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.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: -1.35873668540194 instead of -3.41025189653382 +-feature swap of score: -1.26808971511229 instead of -3.25736799712434 +-feature swap of score: -1.96675515778668 instead of -3.031555020097 +-feature swap of score: -1.34533862547164 instead of -1.81086250492247 +-feature swap of score: -1.06240723671118 instead of -1.27967022783124 +-feature swap of score: -0.649426435234051 instead of -0.969052293093307 +-feature swap of score: 1.89196028351922 instead of -2.15814773715252 +-feature swap of score: -1.05675171308534 instead of -1.5564657682727 +-feature swap of score: 2.54032214550815 instead of -1.46508265510934 +-feature swap of score: 1.36282529462574 instead of -1.17419281204929 +-feature swap of score: -0.568344137392056 instead of -1.16048976677113 +-feature swap of score: 0.0879321507069827 instead of -1.0475947929075 +-feature swap of score: 0.744850915819374 instead of -1.18171313823738 +-feature swap of score: 1.99607816512683 instead of -1.20651022079654 +-feature swap of score: 0.780649280379026 instead of -0.942813926623949 +-feature swap of score: -0.342383969073228 instead of -1.08430127837368 +-feature swap of score: 1.07484243630531 instead of -1.07280545027556 +-feature swap of score: -0.111056732529513 instead of -0.873698373965854 +-feature swap of score: -0.65641663028238 instead of -0.995267217188951 +-feature swap of score: 0.44984777765308 instead of -0.604982587991814 +-feature swap of score: 3.19997128341984 instead of -0.309829137861709 +-feature swap of score: 1.51846040196079 instead of -0.227545893845252 +-feature swap of score: 2.67318365543789 instead of -0.199224167240428 +-feature swap of score: 0.277231416970389 instead of -0.370631678798151 +-feature swap of score: 2.62199485966814 instead of -0.478670338355936 +-feature swap of score: 2.31648120585462 instead of -0.15455666685368 +-feature swap of score: 1.51234372662018 instead of -0.085830750109178 +-feature swap of score: -0.417445142235902 instead of -0.420810447217107 +-feature swap of score: 2.03857495044575 instead of -0.259424879192195 +-feature swap of score: -0.193153078987588 instead of -0.312300883708471 +-feature swap of score: 0.552576300854591 instead of -0.49649231239101 +-feature swap of score: 1.03952719757889 instead of -0.502136860950095 +-feature swap of score: 2.22678778381024 instead of -0.483434412177307 +-feature swap of score: 0.948846384107162 instead of -0.07623318549702 +-feature swap of score: 1.12475633148843 instead of -0.283241922418101 +-feature swap of score: 1.9043309081529 instead of -0.581432938916493 +-feature swap of score: 0.70953747512672 instead of -0.233950099290747 +-feature swap of score: 2.14360851528955 instead of -0.229101661613043 +-feature swap of score: 0.445770946619841 instead of -0.0838727161267692 +-feature swap of score: 0.115003689518047 instead of -0.131501527446423 +-feature swap of score: 2.97171174020393 instead of -0.114074519330434 +-feature swap of score: 0.45001114179048 instead of -0.00805771163331392 +-feature swap of score: 2.00566061095403 instead of 0.0859028878634016 +-feature swap of score: 2.24805267852098 instead of 0.423878000344003 +-feature swap of score: 1.14058446568648 instead of 0.368378215933947 +-feature swap of score: 2.76625428372871 instead of -0.775982776628679 +-feature swap of score: 0.498411713382761 instead of 0.02407914776169 +-feature swap of score: 2.837931135197 instead of 0.671415056069744 +-feature swap of score: 3.19256296349037 instead of 0.675748166476729 +-feature swap of score: 1.88965714386249 instead of 0.780653427929289 +-feature swap of score: 3.21759232691879 instead of 0.506672394258564 +-feature swap of score: 5.22145899527145 instead of 0.961812089603554 +-feature swap of score: 0.502397790662983 instead of 0.370171927992878 +-feature swap of score: 6.48103613840895 instead of 0.781001039647777 +-feature swap of score: 3.23241315943394 instead of 0.653251202762727 +-num feature swaps: 55 +* [Tue Oct 20 11:37:28 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/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 -* [Tue Sep 16 03:04:36 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 +* [Tue Oct 20 11:37:55 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 -parsing scores -* [Tue Sep 16 03:04:43 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 || : +* [Tue Oct 20 11:38:02 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Tue Sep 16 03:04:44 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 +* [Tue Oct 20 11:38:03 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Tue Sep 16 03:04:45 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 || : +* [Tue Oct 20 11:38:05 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 || : Loading required package: grid null device 1 -* [Tue Sep 16 03:04:45 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 +* [Tue Oct 20 11:38:05 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 Refining start codon selections. --number of revised start positions: 14 -* [Tue Sep 16 03:04:46 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* [Tue Sep 16 03:04:46 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 +-number of revised start positions: 13 +* [Tue Oct 20 11:38:06 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* [Tue Oct 20 11:38:06 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Tue Sep 16 03:04:46 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 +* [Tue Oct 20 11:38:06 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/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 -* [Tue Sep 16 03:04:46 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 +* [Tue Oct 20 11:38:06 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/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.* @@ -13686,9 +13719,9 @@ -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.p7. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-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 [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. @@ -13829,12 +13862,14 @@ 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/820938/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/820938/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/2416656 and its subdirectories -I: Current time: Tue Sep 16 03:05:02 -12 2025 -I: pbuilder-time-stamp: 1758035102 +I: removing directory /srv/workspace/pbuilder/820938 and its subdirectories +I: Current time: Tue Oct 20 11:38:46 +14 2026 +I: pbuilder-time-stamp: 1792445926