Diff of the two buildlogs: -- --- b1/build.log 2025-02-28 20:52:33.325837765 +0000 +++ b2/build.log 2025-02-28 21:01:05.702929260 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 28 08:43:48 -12 2025 -I: pbuilder-time-stamp: 1740775428 +I: Current time: Fri Apr 3 17:15:37 +14 2026 +I: pbuilder-time-stamp: 1775186137 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3680447/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/352007/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Apr 3 03:15 /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/352007/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/352007/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='8c36a505c9544714a9448afc566a24e0' - 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='3680447' - PS1='# ' - PS2='> ' + INVOCATION_ID=4c36982b3631474985ee5922cf7fe643 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=352007 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.PmW6xXY5/pbuilderrc_pnRB --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PmW6xXY5/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.PmW6xXY5/pbuilderrc_wdPE --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PmW6xXY5/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3680447/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/352007/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -284,7 +316,7 @@ Get: 163 http://deb.debian.org/debian trixie/main arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [425 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 125 MB in 1s (151 MB/s) +Fetched 125 MB in 1s (220 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19916 files and directories currently installed.) @@ -838,8 +870,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 28 20:44:41 UTC 2025. -Universal Time is now: Fri Feb 28 20:44:41 UTC 2025. +Local time is now: Fri Apr 3 03:16:07 UTC 2026. +Universal Time is now: Fri Apr 3 03:16:07 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14+b1) ... @@ -989,7 +1021,11 @@ 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/352007/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/352007/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 @@ -1052,7 +1088,7 @@ ## 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 -* [Fri Feb 28 08:44:58 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 +* [Fri Apr 3 17:16:31 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. @@ -1104,13 +1140,13 @@ fi -Building a new DB, current time: 02/28/2025 08:44:58 +Building a new DB, current time: 04/03/2026 17:16:31 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 0.00727415 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00883794 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1185,8 +1221,8 @@ 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: 1848.60 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1389.35 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1243,8 +1279,8 @@ 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: 1979.83 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 849.34 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1309,7 +1345,7 @@ 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: 2349.81 +# Mc/sec: 967.07 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1369,8 +1405,8 @@ 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: 2308.71 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 937.83 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1430,8 +1466,8 @@ 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: 847.05 +# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 317.88 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1481,8 +1517,8 @@ 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: 597.24 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 264.78 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1547,7 +1583,7 @@ 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: 2292.98 +# Mc/sec: 993.71 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1599,8 +1635,8 @@ 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: 685.57 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 276.58 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1650,8 +1686,8 @@ 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: 1624.83 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 918.66 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1707,8 +1743,8 @@ 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: 2380.15 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1047.99 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1796,8 +1832,8 @@ 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: 1636.71 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 741.52 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1881,8 +1917,8 @@ 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: 1927.78 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 845.10 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1938,8 +1974,8 @@ 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: 1159.05 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 452.14 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1995,8 +2031,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1144.64 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 449.34 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2052,8 +2088,8 @@ 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: 3429.42 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1351.46 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2098,7 +2134,7 @@ 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: 2810.16 +# Mc/sec: 1089.82 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2151,7 +2187,7 @@ 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: 3679.87 +# Mc/sec: 1399.23 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2195,8 +2231,8 @@ 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: 1963.26 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 887.74 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2256,8 +2292,8 @@ 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: 1871.17 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 678.69 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2307,8 +2343,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1100.60 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 584.12 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2420,8 +2456,8 @@ 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: 1331.68 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 519.96 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2467,8 +2503,8 @@ 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: 2043.50 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1050.72 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2535,7 +2571,7 @@ 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: 2417.29 +# Mc/sec: 964.60 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2573,8 +2609,8 @@ 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: 4924.74 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1791.51 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2650,8 +2686,8 @@ 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: 1917.66 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 764.58 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2704,7 +2740,7 @@ 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: 2930.40 +# Mc/sec: 1224.76 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2788,8 +2824,8 @@ 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: 555.04 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 217.43 // Query: DLH [M=217] Accession: PF01738.17 @@ -2837,7 +2873,7 @@ 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: 2910.73 +# Mc/sec: 1545.61 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2884,7 +2920,7 @@ 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: 2529.22 +# Mc/sec: 951.65 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2934,7 +2970,7 @@ 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: 3455.62 +# Mc/sec: 1248.07 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2976,8 +3012,8 @@ 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: 4305.25 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1572.51 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3023,7 +3059,7 @@ 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: 1427.53 +# Mc/sec: 581.14 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3060,8 +3096,8 @@ 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: 3628.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1421.82 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3112,8 +3148,8 @@ 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: 1700.33 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 709.24 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3151,7 +3187,7 @@ 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: 2288.88 +# Mc/sec: 815.09 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3189,7 +3225,7 @@ 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: 4314.64 +# Mc/sec: 1535.67 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3240,7 +3276,7 @@ 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: 2782.46 +# Mc/sec: 1201.17 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3278,7 +3314,7 @@ 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: 5479.21 +# Mc/sec: 1952.27 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3338,8 +3374,8 @@ 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: 1853.93 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1073.71 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3384,7 +3420,7 @@ 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: 3044.36 +# Mc/sec: 1319.55 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3440,8 +3476,8 @@ 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: 2475.13 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1087.97 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3495,8 +3531,8 @@ 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: 1042.88 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 399.02 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3533,8 +3569,8 @@ 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: 3479.43 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1824.06 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3610,8 +3646,8 @@ 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: 1099.14 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1163.67 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3675,8 +3711,8 @@ 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: 00:00:00.01 -# Mc/sec: 440.76 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 341.26 // Query: FPP [M=866] Accession: PF05911.10 @@ -3726,8 +3762,8 @@ 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: 2769.21 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 1058.92 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3780,7 +3816,7 @@ 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: 2465.20 +# Mc/sec: 1164.89 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3903,8 +3939,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 770.89 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 297.51 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3943,7 +3979,7 @@ 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: 2001.28 +# Mc/sec: 800.96 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4033,8 +4069,8 @@ 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: 982.01 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 387.24 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4084,8 +4120,8 @@ 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: 591.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 259.15 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4146,7 +4182,7 @@ 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: 1939.18 +# Mc/sec: 744.15 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4250,8 +4286,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1068.11 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 391.46 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4298,8 +4334,8 @@ 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: 2988.98 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1343.45 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4373,8 +4409,8 @@ 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: 1640.48 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 612.96 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4445,7 +4481,7 @@ 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: 1666.52 +# Mc/sec: 927.28 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4492,8 +4528,8 @@ 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: 1276.60 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 470.57 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4563,8 +4599,8 @@ 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 427.30 +# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 +# Mc/sec: 154.30 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4615,7 +4651,7 @@ 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: 1262.76 +# Mc/sec: 1474.34 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4665,8 +4701,8 @@ 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: 4260.08 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1652.26 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4705,7 +4741,7 @@ 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: 1455.12 +# Mc/sec: 981.05 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4750,7 +4786,7 @@ 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: 2670.75 +# Mc/sec: 1007.21 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4801,8 +4837,8 @@ 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: 2126.05 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 790.03 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4884,8 +4920,8 @@ 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: 00:00:00.00 -# Mc/sec: 1475.89 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 566.91 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4985,8 +5021,8 @@ 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: 00:00:00.03 -# Mc/sec: 509.09 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 441.91 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5040,8 +5076,8 @@ 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: 00:00:00.02 -# Mc/sec: 225.97 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 701.52 // Query: IBR [M=62] Accession: PF01485.20 @@ -5078,8 +5114,8 @@ 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: 00:00:00.02 -# Mc/sec: 81.12 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 912.10 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5126,8 +5162,8 @@ 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: 00:00:00.02 -# Mc/sec: 423.01 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1057.68 // Query: malic [M=182] Accession: PF00390.18 @@ -5165,8 +5201,8 @@ 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: 00:00:00.02 -# Mc/sec: 279.13 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2060.48 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5203,8 +5239,8 @@ 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: 00:00:00.03 -# Mc/sec: 256.09 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 591.07 // Query: MatE [M=161] Accession: PF01554.17 @@ -5288,8 +5324,8 @@ 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: 00:00:00.02 -# Mc/sec: 208.38 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 698.98 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5326,8 +5362,8 @@ 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: 00:00:00.02 -# Mc/sec: 820.55 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1681.18 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5501,8 +5537,8 @@ 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.08 -# Mc/sec: 137.85 +# CPU time: 0.09u 0.00s 00:00:00.09 Elapsed: 00:00:00.08 +# Mc/sec: 128.01 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5544,8 +5580,8 @@ 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: 00:00:00.01 -# Mc/sec: 957.37 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1135.12 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5601,8 +5637,8 @@ 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: 00:00:00.02 -# Mc/sec: 442.32 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 597.07 // Query: MIP [M=227] Accession: PF00230.19 @@ -5652,8 +5688,8 @@ 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: 00:00:00.02 -# Mc/sec: 298.16 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1276.78 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5705,8 +5741,8 @@ 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: 00:00:00.02 -# Mc/sec: 153.82 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 711.36 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5796,8 +5832,8 @@ 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: 00:00:00.02 -# Mc/sec: 425.94 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1048.40 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5834,8 +5870,8 @@ 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: 00:00:00.01 -# Mc/sec: 145.23 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1027.87 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5872,8 +5908,8 @@ 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: 3899.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1599.51 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5925,8 +5961,8 @@ 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: 3161.71 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1278.27 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5964,7 +6000,7 @@ 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: 4455.07 +# Mc/sec: 1817.73 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6084,8 +6120,8 @@ 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: 809.89 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 525.43 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6136,7 +6172,7 @@ 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: 2751.61 +# Mc/sec: 1109.69 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6207,7 +6243,7 @@ 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: 1774.83 +# Mc/sec: 1029.63 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6260,7 +6296,7 @@ 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: 1369.50 +# Mc/sec: 1209.57 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6322,8 +6358,8 @@ 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: 2103.90 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 780.93 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6425,8 +6461,8 @@ 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 343.37 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 134.52 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6473,8 +6509,8 @@ 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: 00:00:00.01 -# Mc/sec: 579.08 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1248.35 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6524,8 +6560,8 @@ 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: 00:00:00.02 -# Mc/sec: 66.94 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 768.75 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6575,8 +6611,8 @@ 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: 00:00:00.02 -# Mc/sec: 109.73 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1048.46 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6626,8 +6662,8 @@ 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: 00:00:00.02 -# Mc/sec: 229.69 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1497.31 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6672,7 +6708,7 @@ 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: 839.46 +# Mc/sec: 1553.22 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6718,8 +6754,8 @@ 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: 00:00:00.01 -# Mc/sec: 74.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 779.08 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6783,8 +6819,8 @@ 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: 00:00:00.02 -# Mc/sec: 148.72 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 287.57 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6828,8 +6864,8 @@ 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: 1901.62 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1024.85 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6882,7 +6918,7 @@ 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: 1263.01 +# Mc/sec: 476.24 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6926,8 +6962,8 @@ 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: 00:00:00.01 -# Mc/sec: 260.20 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1567.08 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7027,8 +7063,8 @@ 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: 00:00:00.03 -# Mc/sec: 433.79 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 291.64 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7072,8 +7108,8 @@ 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: 255.36 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 370.37 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7126,7 +7162,7 @@ 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: 3111.67 +# Mc/sec: 1256.21 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7199,8 +7235,8 @@ 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: 530.62 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 209.28 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7260,8 +7296,8 @@ 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: 00:00:00.01 -# Mc/sec: 333.50 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1121.10 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7306,7 +7342,7 @@ 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: 2763.49 +# Mc/sec: 1163.09 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7359,7 +7395,7 @@ 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: 2483.59 +# Mc/sec: 1149.12 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7397,7 +7433,7 @@ 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: 6978.40 +# Mc/sec: 2842.33 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7440,7 +7476,7 @@ 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: 3508.83 +# Mc/sec: 1544.30 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7502,8 +7538,8 @@ 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: 1025.77 +# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 +# Mc/sec: 416.92 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7541,7 +7577,7 @@ 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: 2604.48 +# Mc/sec: 1719.20 // Query: Usher [M=551] Accession: PF00577.19 @@ -7585,8 +7621,8 @@ 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: 3120.20 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1407.57 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7633,7 +7669,7 @@ 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: 207.91 +# Mc/sec: 463.00 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7678,7 +7714,7 @@ 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: 402.00 +# Mc/sec: 459.42 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7722,8 +7758,8 @@ 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: 993.76 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 482.93 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7778,7 +7814,7 @@ 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: 1060.21 +# Mc/sec: 546.94 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7816,8 +7852,8 @@ 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: 00:00:00.02 -# Mc/sec: 81.22 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 469.65 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7869,7 +7905,7 @@ 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: 145.13 +# Mc/sec: 493.93 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7916,8 +7952,8 @@ 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: 492.07 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 742.25 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7956,14 +7992,14 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 207.72 +# Mc/sec: 683.49 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Fri Feb 28 08:45:00 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 -* [Fri Feb 28 08:45:00 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 +* [Fri Apr 3 17:16:33 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 +* [Fri Apr 3 17:16:33 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 @@ -7990,39 +8026,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Fri Feb 28 08:45:00 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 +* [Fri Apr 3 17:16:33 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 -* [Fri Feb 28 08:45:00 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 -* [Fri Feb 28 08:45:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Fri Feb 28 08:45:01 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 +* [Fri Apr 3 17:16:34 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 +* [Fri Apr 3 17:16:34 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/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 +* [Fri Apr 3 17:16:35 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... -* [Fri Feb 28 08:45:01 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* [Fri Feb 28 08:45:01 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 -* [Fri Feb 28 08:45:01 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 +* [Fri Apr 3 17:16:35 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* [Fri Apr 3 17:16:35 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 +* [Fri Apr 3 17:16:35 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 -* [Fri Feb 28 08:45:17 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 +* [Fri Apr 3 17:16:50 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 -* [Fri Feb 28 08:45:21 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 || : +* [Fri Apr 3 17:16:54 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 -* [Fri Feb 28 08:45:22 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 +* [Fri Apr 3 17:16:55 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 -* [Fri Feb 28 08:45:23 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 || : +* [Fri Apr 3 17:16:56 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 -* [Fri Feb 28 08:45:24 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 || : +* [Fri Apr 3 17:16:57 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 -* [Fri Feb 28 08:45:24 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 +* [Fri Apr 3 17:16:58 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 @@ -8032,33 +8068,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Fri Feb 28 08:45:24 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 +* [Fri Apr 3 17:16:58 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 -* [Fri Feb 28 08:45:39 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 +* [Fri Apr 3 17:17:13 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 -* [Fri Feb 28 08:45:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Fri Apr 3 17:17:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 08:45:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Fri Apr 3 17:17:18 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 -* [Fri Feb 28 08:45:46 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 || : +* [Fri Apr 3 17:17:19 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 -* [Fri Feb 28 08:45:46 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 +* [Fri Apr 3 17:17:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Fri Feb 28 08:45:46 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* [Fri Feb 28 08:45:47 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 +* [Fri Apr 3 17:17:19 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* [Fri Apr 3 17:17:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Fri Feb 28 08:45:47 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 +* [Fri Apr 3 17:17:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Fri Feb 28 08:45:47 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 +* [Fri Apr 3 17:17:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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.* @@ -8150,7 +8186,7 @@ ../../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 -* [Fri Feb 28 08:45:47 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 +* [Fri Apr 3 17:17:20 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. @@ -8174,8 +8210,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Fri Feb 28 08:45:49 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 -* [Fri Feb 28 08:45:49 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 +* [Fri Apr 3 17:17:22 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 +* [Fri Apr 3 17:17:22 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 @@ -8850,37 +8886,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Fri Feb 28 08:45:50 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 +* [Fri Apr 3 17:17:23 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 -* [Fri Feb 28 08:45:50 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 -* [Fri Feb 28 08:45:51 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 -* [Fri Feb 28 08:45:58 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 +* [Fri Apr 3 17:17:23 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 +* [Fri Apr 3 17:17:24 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 +* [Fri Apr 3 17:17:31 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 -* [Fri Feb 28 08:45:58 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* [Fri Feb 28 08:45:58 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 -* [Fri Feb 28 08:45:59 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 +* [Fri Apr 3 17:17:31 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* [Fri Apr 3 17:17:31 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 +* [Fri Apr 3 17:17:32 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 -* [Fri Feb 28 08:46:23 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 +* [Fri Apr 3 17:17:55 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/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 -* [Fri Feb 28 08:46:29 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 || : +* [Fri Apr 3 17:18:01 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 -* [Fri Feb 28 08:46:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Fri Apr 3 17:18:02 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 -* [Fri Feb 28 08:46:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Fri Apr 3 17:18:03 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 -* [Fri Feb 28 08:46:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Fri Apr 3 17:18:04 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 08:46:33 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 +* [Fri Apr 3 17:18:05 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 @@ -8939,33 +8975,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Fri Feb 28 08:46:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Fri Apr 3 17:18:05 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 -* [Fri Feb 28 08:46:59 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 +* [Fri Apr 3 17:18:33 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.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 -* [Fri Feb 28 08:47:04 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 || : +* [Fri Apr 3 17:18:39 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 -* [Fri Feb 28 08:47:06 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 +* [Fri Apr 3 17:18:40 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 -* [Fri Feb 28 08:47:07 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 || : +* [Fri Apr 3 17:18:41 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 -* [Fri Feb 28 08:47:07 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 +* [Fri Apr 3 17:18:42 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 -* [Fri Feb 28 08:47:08 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* [Fri Feb 28 08:47:08 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 +* [Fri Apr 3 17:18:42 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* [Fri Apr 3 17:18:42 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 -* [Fri Feb 28 08:47:08 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/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 +* [Fri Apr 3 17:18:42 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 -* [Fri Feb 28 08:47:08 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/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 +* [Fri Apr 3 17:18:43 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.* @@ -8986,8 +9022,8 @@ -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. --Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. +-Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 107, 466 @@ -9022,8 +9058,8 @@ CDS coords: 80, 427 -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). --Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. --Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 112, 447 @@ -9058,7 +9094,7 @@ 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 -* [Fri Feb 28 08:47:09 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 +* [Fri Apr 3 17:18:44 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. @@ -9078,8 +9114,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Fri Feb 28 08:47:11 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 -* [Fri Feb 28 08:47:11 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 +* [Fri Apr 3 17:18:46 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 +* [Fri Apr 3 17:18:46 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 @@ -9117,37 +9153,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Fri Feb 28 08:47:12 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 +* [Fri Apr 3 17:18:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Fri Feb 28 08:47:12 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 -* [Fri Feb 28 08:47:14 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 -* [Fri Feb 28 08:47:22 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 +* [Fri Apr 3 17:18:47 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 +* [Fri Apr 3 17:18:49 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 +* [Fri Apr 3 17:18:56 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 -* [Fri Feb 28 08:47:22 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* [Fri Feb 28 08:47:22 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 -* [Fri Feb 28 08:47:22 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 +* [Fri Apr 3 17:18:56 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* [Fri Apr 3 17:18:56 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 +* [Fri Apr 3 17:18:57 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 -* [Fri Feb 28 08:47:47 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 +* [Fri Apr 3 17:19:21 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/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 -* [Fri Feb 28 08:47:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Fri Apr 3 17:19:27 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 -* [Fri Feb 28 08:47:55 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 +* [Fri Apr 3 17:19:28 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 -* [Fri Feb 28 08:47:56 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 || : +* [Fri Apr 3 17:19:29 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 -* [Fri Feb 28 08:47:57 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 || : +* [Fri Apr 3 17:19:30 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 08:47:57 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 +* [Fri Apr 3 17:19:31 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 @@ -9253,33 +9289,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Fri Feb 28 08:47:58 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 +* [Fri Apr 3 17:19:31 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 -* [Fri Feb 28 08:48:21 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 +* [Fri Apr 3 17:19:54 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/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 -* [Fri Feb 28 08:48:27 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 || : +* [Fri Apr 3 17:20:00 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 -* [Fri Feb 28 08:48:28 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 +* [Fri Apr 3 17:20:01 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 -* [Fri Feb 28 08:48:29 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 || : +* [Fri Apr 3 17:20:02 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 -* [Fri Feb 28 08:48:30 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 +* [Fri Apr 3 17:20:03 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 -* [Fri Feb 28 08:48:30 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* [Fri Feb 28 08:48:30 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 +* [Fri Apr 3 17:20:03 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* [Fri Apr 3 17:20:03 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 -* [Fri Feb 28 08:48:30 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 +* [Fri Apr 3 17:20:03 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 -* [Fri Feb 28 08:48:30 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 +* [Fri Apr 3 17:20:04 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.* @@ -9296,32 +9332,32 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', + 'gene_id' => '', + 'asmbl' => 'comp1051_c1_seq1', + 'orient' => '-', 'coords' => [ [ '1642973', '1644586' ] ], - 'asmbl' => 'comp1051_c1_seq1', - 'gene_id' => '', 'trans_id' => '', - 'orient' => '-' + 'contig' => 'III' }; + is_pseudogene: 0 + gene_type: protein-coding + is_5prime_partial: 0 Model_feat_name: comp1051_c1_seq1.p1 - com_name: ORF type:5prime_partial (+),score=83.26 + classification: annotated_genes + num_exons: 1 + gene_length: 1616 + strand: + + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 asmbl_id: comp1051_c1_seq1 is_3prime_partial: 0 mid_pt: 808 - strand: + + com_name: ORF type:5prime_partial (+),score=83.26 source: transdecoder - is_5prime_partial: 0 - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 - gene_type: protein-coding - classification: annotated_genes - num_exons: 1 - gene_length: 1616 - is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9338,9 +9374,8 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', + 'contig' => 'I', 'trans_id' => '', - 'asmbl' => 'comp1058_c0_seq1', 'coords' => [ [ 5095548, @@ -9351,23 +9386,24 @@ '5095301' ] ], - 'contig' => 'I', - 'gene_id' => '' + 'orient' => '-', + 'gene_id' => '', + 'asmbl' => 'comp1058_c0_seq1' }; - mid_pt: 248 - strand: + source: transdecoder - is_5prime_partial: 0 - Model_feat_name: comp1058_c0_seq1.p1 com_name: ORF type:5prime_partial (+),score=32.57 - asmbl_id: comp1058_c0_seq1 is_3prime_partial: 0 - gene_length: 496 + asmbl_id: comp1058_c0_seq1 + mid_pt: 248 + gene_type: protein-coding + is_5prime_partial: 0 + Model_feat_name: comp1058_c0_seq1.p1 is_pseudogene: 0 + strand: + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 classification: annotated_genes - gene_type: protein-coding num_exons: 1 + gene_length: 496 gene_synonyms: mRNA_coords CDS_coords @@ -9390,9 +9426,8 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', 'gene_id' => '', - 'contig' => 'III', + 'asmbl' => 'comp1112_c0_seq1', 'coords' => [ [ 2380416, @@ -9403,23 +9438,24 @@ '2380336' ] ], - 'asmbl' => 'comp1112_c0_seq1', - 'orient' => '-' + 'orient' => '-', + 'contig' => 'III', + 'trans_id' => '' }; - com_name: ORF type:complete (+),score=155.28 - Model_feat_name: comp1112_c0_seq1.p1 - asmbl_id: comp1112_c0_seq1 - is_3prime_partial: 0 - mid_pt: 1041 - strand: + - is_5prime_partial: 0 - source: transdecoder - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + gene_length: 2081 num_exons: 1 - gene_type: protein-coding classification: annotated_genes - gene_length: 2081 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + strand: + is_pseudogene: 0 + Model_feat_name: comp1112_c0_seq1.p1 + gene_type: protein-coding + is_5prime_partial: 0 + mid_pt: 1041 + is_3prime_partial: 0 + asmbl_id: comp1112_c0_seq1 + source: transdecoder + com_name: ORF type:complete (+),score=155.28 gene_synonyms: mRNA_coords CDS_coords @@ -9441,6 +9477,11 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'asmbl' => 'comp1198_c0_seq1', + 'gene_id' => '', + 'contig' => 'II', + 'trans_id' => '', + 'orient' => '-', 'coords' => [ [ 402195, @@ -9458,27 +9499,22 @@ 401352, '401683' ] - ], - 'asmbl' => 'comp1198_c0_seq1', - 'contig' => 'II', - 'gene_id' => '', - 'trans_id' => '', - 'orient' => '-' + ] }; - gene_length: 597 - is_pseudogene: 0 - gene_type: protein-coding classification: annotated_genes num_exons: 1 + gene_length: 597 + strand: + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - source: transdecoder + is_pseudogene: 0 is_5prime_partial: 0 - mid_pt: 299 - strand: + - is_3prime_partial: 0 + gene_type: protein-coding Model_feat_name: comp1198_c0_seq1.p1 - com_name: ORF type:internal (+),score=37.56 + is_3prime_partial: 0 asmbl_id: comp1198_c0_seq1 + mid_pt: 299 + com_name: ORF type:internal (+),score=37.56 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9506,9 +9542,6 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'trans_id' => '', - 'contig' => 'III', 'coords' => [ [ 368840, @@ -9519,23 +9552,26 @@ '368790' ] ], + 'orient' => '-', + 'contig' => 'III', + 'trans_id' => '', 'asmbl' => 'comp1210_c0_seq1', 'gene_id' => '' }; - gene_length: 1554 is_pseudogene: 0 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 - num_exons: 1 - classification: annotated_genes + Model_feat_name: comp1210_c0_seq1.p1 + is_5prime_partial: 0 gene_type: protein-coding - mid_pt: 777 + gene_length: 1554 + classification: annotated_genes + num_exons: 1 + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 strand: + - is_5prime_partial: 0 - source: transdecoder - com_name: ORF type:5prime_partial (+),score=12.16 - Model_feat_name: comp1210_c0_seq1.p1 - asmbl_id: comp1210_c0_seq1 + mid_pt: 777 is_3prime_partial: 0 + asmbl_id: comp1210_c0_seq1 + com_name: ORF type:5prime_partial (+),score=12.16 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9560,32 +9596,32 @@ -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 = { - 'trans_id' => '', - 'gene_id' => '', - 'contig' => 'II', 'coords' => [ [ '3840968', '3841303' ] ], - 'asmbl' => 'comp366_c0_seq1', - 'orient' => '-' + 'orient' => '-', + 'trans_id' => '', + 'contig' => 'II', + 'gene_id' => '', + 'asmbl' => 'comp366_c0_seq1' }; + gene_length: 340 + num_exons: 1 + classification: annotated_genes + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + strand: - + is_pseudogene: 0 Model_feat_name: comp366_c0_seq1.p1 - com_name: ORF type:internal (-),score=12.83 + gene_type: protein-coding + is_5prime_partial: 0 + mid_pt: 170 asmbl_id: comp366_c0_seq1 is_3prime_partial: 0 - strand: - - mid_pt: 170 + com_name: ORF type:internal (-),score=12.83 source: transdecoder - is_5prime_partial: 0 - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - classification: annotated_genes - gene_type: protein-coding - num_exons: 1 - gene_length: 340 - is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9611,32 +9647,32 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'trans_id' => '', + 'asmbl' => 'comp610_c0_seq1', 'gene_id' => '', - 'contig' => 'I', + 'orient' => '-', 'coords' => [ [ '5471264', '5472770' ] ], - 'asmbl' => 'comp610_c0_seq1' + 'trans_id' => '', + 'contig' => 'I' }; - source: transdecoder + Model_feat_name: comp610_c0_seq1.p1 + gene_type: protein-coding is_5prime_partial: 0 + is_pseudogene: 0 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 strand: + - mid_pt: 755 - is_3prime_partial: 0 - Model_feat_name: comp610_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=50.55 - asmbl_id: comp610_c0_seq1 gene_length: 1509 - is_pseudogene: 0 classification: annotated_genes - gene_type: protein-coding num_exons: 1 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + source: transdecoder + com_name: ORF type:5prime_partial (+),score=50.55 + mid_pt: 755 + asmbl_id: comp610_c0_seq1 + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9655,32 +9691,32 @@ -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 = { - 'orient' => '-', 'gene_id' => '', + 'asmbl' => 'comp645_c0_seq1', 'coords' => [ [ '4333088', '4336727' ] ], - 'asmbl' => 'comp645_c0_seq1', + 'orient' => '-', 'contig' => 'I', 'trans_id' => '' }; - mid_pt: 1827 - strand: + + com_name: ORF type:5prime_partial (+),score=273.35 source: transdecoder - is_5prime_partial: 0 + is_3prime_partial: 0 asmbl_id: comp645_c0_seq1 + mid_pt: 1827 Model_feat_name: comp645_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=273.35 - is_3prime_partial: 0 + gene_type: protein-coding + is_5prime_partial: 0 is_pseudogene: 0 - gene_length: 3653 TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + strand: + classification: annotated_genes - gene_type: protein-coding num_exons: 1 + gene_length: 3653 gene_synonyms: mRNA_coords CDS_coords @@ -9696,9 +9732,8 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '+', - 'gene_id' => '', - 'asmbl' => 'comp688_c0_seq1', + 'trans_id' => '', + 'contig' => 'II', 'coords' => [ [ 380308, @@ -9709,23 +9744,24 @@ '381243' ] ], - 'contig' => 'II', - 'trans_id' => '' + 'orient' => '+', + 'gene_id' => '', + 'asmbl' => 'comp688_c0_seq1' }; is_5prime_partial: 0 - source: transdecoder - mid_pt: 1392 - strand: + - is_3prime_partial: 0 - asmbl_id: comp688_c0_seq1 - com_name: ORF type:complete (+),score=172.54 + gene_type: protein-coding Model_feat_name: comp688_c0_seq1.p1 is_pseudogene: 0 - gene_length: 2784 + strand: + + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 num_exons: 1 - gene_type: protein-coding classification: annotated_genes - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + gene_length: 2784 + source: transdecoder + com_name: ORF type:complete (+),score=172.54 + is_3prime_partial: 0 + asmbl_id: comp688_c0_seq1 + mid_pt: 1392 gene_synonyms: mRNA_coords CDS_coords @@ -9749,9 +9785,9 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '+', 'trans_id' => '', - 'asmbl' => 'comp856_c0_seq1', + 'contig' => 'II', + 'orient' => '+', 'coords' => [ [ 3753910, @@ -9762,23 +9798,23 @@ '3755057' ] ], - 'contig' => 'II', - 'gene_id' => '' + 'gene_id' => '', + 'asmbl' => 'comp856_c0_seq1' }; - source: transdecoder - is_5prime_partial: 0 - mid_pt: 785 - strand: + - is_3prime_partial: 0 - Model_feat_name: comp856_c0_seq1.p1 - com_name: ORF type:complete (+),score=71.94 - asmbl_id: comp856_c0_seq1 gene_length: 1569 - is_pseudogene: 0 - gene_type: protein-coding classification: annotated_genes num_exons: 1 TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + strand: + + is_pseudogene: 0 + Model_feat_name: comp856_c0_seq1.p1 + is_5prime_partial: 0 + gene_type: protein-coding + mid_pt: 785 + asmbl_id: comp856_c0_seq1 + is_3prime_partial: 0 + com_name: ORF type:complete (+),score=71.94 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9798,10 +9834,11 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'trans_id' => '', 'gene_id' => '', 'asmbl' => 'comp873_c0_seq2', + 'trans_id' => '', + 'contig' => 'II', + 'orient' => '-', 'coords' => [ [ 3727877, @@ -9815,23 +9852,22 @@ 3726988, '3727657' ] - ], - 'contig' => 'II' + ] }; - is_3prime_partial: 0 Model_feat_name: comp873_c0_seq2.p1 - com_name: ORF type:5prime_partial (+),score=8.59 - asmbl_id: comp873_c0_seq2 - source: transdecoder + gene_type: protein-coding is_5prime_partial: 0 - mid_pt: 513 + is_pseudogene: 0 + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 strand: + - gene_type: protein-coding classification: annotated_genes num_exons: 1 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 gene_length: 1025 - is_pseudogene: 0 + source: transdecoder + com_name: ORF type:5prime_partial (+),score=8.59 + asmbl_id: comp873_c0_seq2 + is_3prime_partial: 0 + mid_pt: 513 gene_synonyms: mRNA_coords CDS_coords @@ -9856,7 +9892,8 @@ Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', - 'asmbl' => 'comp888_c0_seq1', + 'contig' => 'III', + 'orient' => '-', 'coords' => [ [ 1268244, @@ -9867,24 +9904,23 @@ '1268172' ] ], - 'contig' => 'III', 'gene_id' => '', - 'orient' => '-' + 'asmbl' => 'comp888_c0_seq1' }; - mid_pt: 295 strand: + + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 + gene_length: 589 + num_exons: 1 + classification: annotated_genes is_5prime_partial: 0 - source: transdecoder - com_name: ORF type:5prime_partial (+),score=23.94 + gene_type: protein-coding Model_feat_name: comp888_c0_seq1.p1 + is_pseudogene: 0 + com_name: ORF type:5prime_partial (+),score=23.94 + source: transdecoder + mid_pt: 295 asmbl_id: comp888_c0_seq1 is_3prime_partial: 0 - gene_length: 589 - is_pseudogene: 0 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 - num_exons: 1 - gene_type: protein-coding - classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9906,9 +9942,9 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', 'gene_id' => '', - 'contig' => 'III', + 'asmbl' => 'comp940_c0_seq1', + 'orient' => '+', 'coords' => [ [ 105641, @@ -9919,23 +9955,23 @@ '106404' ] ], - 'asmbl' => 'comp940_c0_seq1', - 'orient' => '+' + 'contig' => 'III', + 'trans_id' => '' }; - asmbl_id: comp940_c0_seq1 - Model_feat_name: comp940_c0_seq1.p1 - com_name: ORF type:complete (+),score=94.37 is_3prime_partial: 0 + asmbl_id: comp940_c0_seq1 mid_pt: 1065 - strand: + source: transdecoder + com_name: ORF type:complete (+),score=94.37 + is_pseudogene: 0 + Model_feat_name: comp940_c0_seq1.p1 is_5prime_partial: 0 - TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 gene_type: protein-coding classification: annotated_genes num_exons: 1 - is_pseudogene: 0 gene_length: 2129 + TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9955,7 +9991,8 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'asmbl' => 'comp983_c0_seq1', + 'gene_id' => '', 'coords' => [ [ 4100066, @@ -9966,25 +10003,24 @@ '4100014' ] ], - 'asmbl' => 'comp983_c0_seq1', + 'orient' => '-', 'contig' => 'I', - 'gene_id' => '', - 'orient' => '-' + 'trans_id' => '' }; - source: transdecoder - is_5prime_partial: 0 mid_pt: 935 - strand: + is_3prime_partial: 0 asmbl_id: comp983_c0_seq1 - Model_feat_name: comp983_c0_seq1.p1 com_name: ORF type:5prime_partial (+),score=143.65 - is_pseudogene: 0 + source: transdecoder gene_length: 1870 - gene_type: protein-coding - classification: annotated_genes num_exons: 1 + classification: annotated_genes + strand: + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding + is_5prime_partial: 0 + Model_feat_name: comp983_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -10028,7 +10064,7 @@ ## 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 -* [Fri Feb 28 08:48:32 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 +* [Fri Apr 3 17:20:05 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. @@ -10053,8 +10089,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Fri Feb 28 08:48:45 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 -* [Fri Feb 28 08:48:46 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 +* [Fri Apr 3 17:20:18 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 +* [Fri Apr 3 17:20:18 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 @@ -12672,37 +12708,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Fri Feb 28 08:48:48 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 +* [Fri Apr 3 17:20:21 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 -* [Fri Feb 28 08:48:49 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 -* [Fri Feb 28 08:48:51 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 -* [Fri Feb 28 08:49:36 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 +* [Fri Apr 3 17:20:21 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 +* [Fri Apr 3 17:20:24 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 +* [Fri Apr 3 17:21:05 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 -* [Fri Feb 28 08:49:37 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* [Fri Feb 28 08:49:37 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 -* [Fri Feb 28 08:49:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Fri Apr 3 17:21:06 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* [Fri Apr 3 17:21:06 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 +* [Fri Apr 3 17:21:08 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 -* [Fri Feb 28 08:50:04 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 +* [Fri Apr 3 17:21:33 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/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 -* [Fri Feb 28 08:50:10 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 || : +* [Fri Apr 3 17:21:39 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 -* [Fri Feb 28 08:50:12 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 +* [Fri Apr 3 17:21:40 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 -* [Fri Feb 28 08:50:13 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 || : +* [Fri Apr 3 17:21:41 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 -* [Fri Feb 28 08:50:13 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 || : +* [Fri Apr 3 17:21:42 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 -* [Fri Feb 28 08:50:14 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 +* [Fri Apr 3 17:21:42 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 @@ -12805,33 +12841,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Fri Feb 28 08:50:14 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 +* [Fri Apr 3 17:21:43 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 -* [Fri Feb 28 08:50:38 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 +* [Fri Apr 3 17:22:07 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 -* [Fri Feb 28 08:50:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Fri Apr 3 17:22:13 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 -* [Fri Feb 28 08:50:45 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 +* [Fri Apr 3 17:22:14 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 -* [Fri Feb 28 08:50:46 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 || : +* [Fri Apr 3 17:22:15 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 -* [Fri Feb 28 08:50:46 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 +* [Fri Apr 3 17:22:16 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 -* [Fri Feb 28 08:50:47 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* [Fri Feb 28 08:50:47 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 +* [Fri Apr 3 17:22:17 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* [Fri Apr 3 17:22:17 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 -* [Fri Feb 28 08:50:48 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 +* [Fri Apr 3 17:22:17 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 -* [Fri Feb 28 08:50:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds +* [Fri Apr 3 17:22:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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.* @@ -12943,7 +12979,7 @@ // 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 -* [Fri Feb 28 08:50:56 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 +* [Fri Apr 3 17:22:26 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. @@ -12967,43 +13003,43 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Fri Feb 28 08:50:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 08:50:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Fri Apr 3 17:22:28 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/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 +* [Fri Apr 3 17:22:28 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_i2.p1, not unique enough -skipping training candidate: bdg_i3.p1, not unique enough --skipping training candidate: bdg_i4.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 -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i3.p1, not unique enough +-skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough +-skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: Calx_i4.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: 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_i4.p1, not unique enough +-skipping training candidate: Klp10A_i5.p1, not unique enough -skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: Klp10A_i6.p1, not unique enough -skipping training candidate: Klp10A_i3.p1, not unique enough --skipping training candidate: Klp10A_i5.p1, not unique enough --skipping training candidate: Klp10A_i4.p1, not unique enough --skipping training candidate: Klp10A_i1.p1, not unique enough --skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_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: Dgk_i4.p1, not unique enough -skipping training candidate: CG33970_i2.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough @@ -13011,14 +13047,14 @@ -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_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_i3.p1, not unique enough --skipping training candidate: hrg_i1.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_i3.p1, not unique enough +-skipping training candidate: hrg_i2.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_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p1, not unique enough +-skipping training candidate: Npl4_i1.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough @@ -13030,17 +13066,17 @@ -skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough --skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough +-skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough --skipping training candidate: Est-6_i2.p1, not unique enough +-skipping training candidate: Est-6_i1.p1, not unique enough -skipping training candidate: S-Lap3_i3.p1, not unique enough -skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough --skipping training candidate: CG30438_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: CG30438_i3.p1, not unique enough -skipping training candidate: CG6145_i4.p1, not unique enough @@ -13048,57 +13084,57 @@ -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough -skipping training candidate: Eno_i5.p1, not unique enough --skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i1.p1, not unique enough +-skipping training candidate: Eno_i4.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_i3.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_i4.p1, not unique enough -skipping training candidate: Aldh-III_i6.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: Aldh-III_i8.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: Galk_i4.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_i6.p1, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough +-skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i5.p2, not unique enough --skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: Eno_i1.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_i4.p2, not unique enough +-skipping training candidate: CG6424_i2.p2, not unique enough -skipping training candidate: CG6424_i4.p2, not unique enough +-skipping training candidate: CG6424_i1.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_i4.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: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i5.p1, not unique enough -skipping training candidate: AdipoR_i3.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_i5.p1, not unique enough -skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: Tm1_i14.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: kto_i1.p2, 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_i6.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough +-skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i1.p1, not unique enough --skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: 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_i1.p1, not unique enough +-skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG7564_i3.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough --skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i5.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough +-skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough @@ -13106,9 +13142,9 @@ -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_i6.p1, not unique enough --skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough +-skipping training candidate: ogre_i4.p1, not unique enough -skipping training candidate: ogre_i1.p1, not unique enough -skipping training candidate: ogre_i3.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough @@ -13120,228 +13156,228 @@ -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_i4.p2, not unique enough +-skipping training candidate: Klp10A_i5.p2, not unique enough -skipping training candidate: Klp10A_i2.p2, not unique enough +-skipping training candidate: Klp10A_i6.p2, not unique enough -skipping training candidate: Klp10A_i3.p2, not unique enough --skipping training candidate: Klp10A_i5.p2, not unique enough --skipping training candidate: Klp10A_i4.p2, not unique enough --skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough --skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough +-skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough --skipping training candidate: regucalcin_i1.p1, not unique enough -skipping training candidate: regucalcin_i4.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: CG10237_i3.p1, not unique enough -skipping training candidate: CG10237_i1.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_i3.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: l(3)05822_i3.p2, 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_i11.p1, not unique enough -skipping training candidate: Tm1_i4.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: Npl4_i1.p2, not unique enough -skipping training candidate: Npl4_i2.p2, not unique enough --skipping training candidate: Npl4_i3.p2, not unique enough --skipping training candidate: Sec16_i1.p2, not unique enough --skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough --skipping training candidate: CG8312_i4.p2, not unique enough +-skipping training candidate: Sec16_i5.p2, not unique enough +-skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough --skipping training candidate: Dgk_i1.p2, not unique enough +-skipping training candidate: CG8312_i4.p2, not unique enough +-skipping training candidate: Dgk_i7.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_i3.p2, not unique enough -skipping training candidate: eIF5B_i5.p2, not unique enough --skipping training candidate: eIF5B_i2.p2, not unique enough --skipping training candidate: eIF5B_i4.p2, not unique enough --skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough -skipping training candidate: l(1)G0193_i1.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough --skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough +-skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough --skipping training candidate: Dgk_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: Dgk_i4.p3, not unique enough -skipping training candidate: Dgk_i2.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: l(3)05822_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i2.p2, not unique enough +-skipping training candidate: Sec16_i6.p2, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough --skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG13887_i2.p1, not unique enough -skipping training candidate: CG14995_i7.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough --skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough +-skipping training candidate: nmo_i2.p2, not unique enough +-skipping training candidate: nmo_i4.p2, not unique enough -skipping training candidate: nmo_i3.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_i4.p2, not unique enough --skipping training candidate: nmo_i5.p2, not unique enough --skipping training candidate: nmo_i2.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough --skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: gukh_i1.p2, not unique enough +-skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough --skipping training candidate: RpL15_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_i4.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: RpL15_i1.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: Npl4_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: Hsc70-1_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough --skipping training candidate: CG14995_i4.p2, not unique enough --skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough --skipping training candidate: CG10237_i3.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_i1.p2, not unique enough --skipping training candidate: CG10237_i5.p2, not unique enough --skipping training candidate: Eno_i3.p3, not unique enough --skipping training candidate: Eno_i5.p3, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: Eno_i6.p3, not unique enough -skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i4.p3, not unique enough +-skipping training candidate: Eno_i5.p3, not unique enough -skipping training candidate: Eno_i1.p3, not unique enough +-skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Sec16_i1.p3, not unique enough --skipping training candidate: Sec16_i4.p3, not unique enough +-skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough --skipping training candidate: gukh_i1.p3, not unique enough +-skipping training candidate: gukh_i2.p2, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough -skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: 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_i4.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: CG30438_i3.p2, not unique enough --skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough -skipping training candidate: cdi_i2.p2, not unique enough --skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough --skipping training candidate: CanB2_i2.p1, 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_i3.p2, not unique enough -skipping training candidate: Sec16_i1.p4, not unique enough --skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: bic_i2.p1, not unique enough +-skipping training candidate: Sec16_i3.p3, not unique enough +-skipping training candidate: bic_i1.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_i1.p1, not unique enough --skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: ctp_i2.p1, not unique enough --skipping training candidate: hrg_i3.p2, not unique enough +-skipping training candidate: ctp_i4.p1, not unique enough +-skipping training candidate: ctp_i1.p1, 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_i5.p4, not unique enough +-skipping training candidate: hrg_i3.p2, not unique enough +-skipping training candidate: Eno_i6.p4, not unique enough -skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: Eno_i5.p4, not unique enough -skipping training candidate: Eno_i1.p4, not unique enough +-skipping training candidate: Eno_i4.p4, 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_i2.p4, not unique enough +-skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i3.p3, not unique enough --skipping training candidate: Klp10A_i5.p3, not unique enough --skipping training candidate: Klp10A_i4.p3, not unique enough --skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Calx_i7.p3, 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_i4.p2, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough +-skipping training candidate: Calx_i3.p2, not unique enough -skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: Calx_i1.p2, not unique enough --skipping training candidate: Calx_i2.p2, not unique enough --skipping training candidate: Calx_i8.p2, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough -skipping training candidate: CG7564_i4.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_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough +-skipping training candidate: CG7564_i2.p4, not unique enough +-skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: CG7564_i3.p3, not unique enough -skipping training candidate: Gale_i1.p2, 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_i3.p3, not unique enough -skipping training candidate: eIF5B_i5.p3, not unique enough --skipping training candidate: eIF5B_i2.p3, not unique enough --skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: 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_i1.p3, not unique enough --skipping training candidate: CG6424_i3.p3, not unique enough --skipping training candidate: CG6424_i3.p4, 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_i4.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: Tm1_i13.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: Tm1_i16.p2, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough -skipping training candidate: Dgk_i6.p4, not unique enough --skipping training candidate: Dgk_i1.p4, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough -skipping training candidate: Dgk_i2.p5, not unique enough +-skipping training candidate: Dgk_i7.p5, not unique enough -skipping training candidate: cdi_i2.p3, not unique enough --skipping training candidate: eff_i3.p1, not unique enough +-skipping training candidate: eff_i2.p1, not unique enough -skipping training candidate: eff_i1.p1, not unique enough -skipping training candidate: CG6852_i2.p1, 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_i3.p4, not unique enough -skipping training candidate: eIF5B_i5.p4, not unique enough --skipping training candidate: eIF5B_i2.p4, not unique enough --skipping training candidate: eIF5B_i4.p5, 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_i4.p5, not unique enough +-skipping training candidate: Sec16_i6.p3, not unique enough -skipping training candidate: Sec16_i5.p4, not unique enough --skipping training candidate: Sec16_i2.p5, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough -skipping training candidate: CG32082_i1.p2, not unique enough --skipping training candidate: CG32082_i2.p2, not unique enough --skipping training candidate: CG3530_i1.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough --skipping training candidate: Dgk_i2.p6, not unique enough +-skipping training candidate: CG3530_i1.p2, not unique enough +-skipping training candidate: Dgk_i7.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: l(3)05822_i3.p4, 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_i1.p4, not unique enough +-skipping training candidate: CG7564_i2.p6, not unique enough -skipping training candidate: CG7564_i3.p4, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough -skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: cdi_i2.p4, not unique enough --skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: CG6091_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough --skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough -skipping training candidate: Cnx99A_i2.p2, not unique enough --skipping training candidate: Sec16_i6.p4, not unique enough --skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough +-skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: ogre_i3.p2, not unique enough -skipping training candidate: CG6024_i2.p3, not unique enough --skipping training candidate: hrg_i1.p3, not unique enough -skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: hrg_i3.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_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough -skipping training candidate: CG33970_i2.p2, not unique enough @@ -13349,315 +13385,318 @@ -skipping training candidate: eIF5B_i1.p5, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: eIF5B_i5.p5, not unique enough --skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i3.p2, not unique enough +-skipping training candidate: Aldh-III_i8.p2, not unique enough +-skipping training candidate: CG13284_i4.p2, not unique enough -skipping training candidate: CG13284_i1.p2, not unique enough --skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: CG13284_i2.p2, not unique enough +-skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: Lip4_i2.p2, not unique enough --skipping training candidate: Lip4_i1.p2, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Lip4_i3.p2, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough --skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough +-skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Tm1_i13.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: Tm1_i16.p3, not unique enough --skipping training candidate: CG8312_i2.p3, not unique enough --skipping training candidate: CG8312_i2.p4, not unique enough --skipping training candidate: CG8312_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough -skipping training candidate: CG8312_i3.p3, not unique enough -skipping training candidate: CG8312_i3.p4, not unique enough +-skipping training candidate: CG8312_i1.p2, not unique enough +-skipping training candidate: CG8312_i1.p3, 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_i4.p4, not unique enough +-skipping training candidate: Klp10A_i5.p4, not unique enough -skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i3.p4, not unique enough --skipping training candidate: Klp10A_i5.p4, not unique enough --skipping training candidate: Klp10A_i4.p4, not unique enough --skipping training candidate: Klp10A_i1.p4, not unique enough --skipping training candidate: eff_i3.p2, not unique enough +-skipping training candidate: eff_i2.p2, not unique enough -skipping training candidate: eff_i1.p2, 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_i1.p4, not unique enough --skipping training candidate: CG14995_i5.p5, not unique enough +-skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough --skipping training candidate: CG14995_i6.p4, not unique enough --skipping training candidate: CG6424_i1.p5, not unique enough --skipping training candidate: CG6424_i3.p5, not unique enough +-skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i4.p4, not unique enough +-skipping training candidate: CG6424_i1.p5, not unique enough -skipping training candidate: CG12581_i1.p3, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: CG32082_i1.p3, not unique enough --skipping training candidate: CG32082_i2.p3, not unique enough --skipping training candidate: Cnx99A_i1.p3, not unique enough -skipping training candidate: Cnx99A_i2.p3, not unique enough +-skipping training candidate: Cnx99A_i3.p3, not unique enough +-skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough --skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough -skipping training candidate: CG33970_i2.p3, not unique enough -skipping training candidate: CG33970_i3.p3, 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_i4.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_i5.p6, not unique enough --skipping training candidate: Sec16_i2.p7, not unique enough +-skipping training candidate: Sec16_i1.p7, not unique enough +-skipping training candidate: Sec16_i3.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: Myo61F_i3.p2, not unique enough --skipping training candidate: Myo61F_i1.p2, not unique enough +-skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Myo61F_i2.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_i1.p4, not unique enough -skipping training candidate: Cnx99A_i2.p4, not unique enough +-skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG13887_i4.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough --skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG13887_i2.p2, not unique enough -skipping training candidate: CG6145_i4.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG6145_i3.p2, not unique enough -skipping training candidate: Calx_i7.p5, 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_i4.p3, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough +-skipping training candidate: Calx_i3.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough -skipping training candidate: Calx_i1.p3, not unique enough --skipping training candidate: Calx_i2.p3, not unique enough --skipping training candidate: Calx_i8.p3, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: mge_i1.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_i1.p2, not unique enough --skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: Aldh-III_i2.p2, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough --skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Aldh-III_i10.p3, not unique enough +-skipping training candidate: Aldh-III_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i2.p2, not unique enough -skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough +-skipping training candidate: Cdep_i2.p9, 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_i3.p4, not unique enough --skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i4.p4, not unique enough --skipping training candidate: CG33125_i2.p2, not unique enough +-skipping training candidate: hrg_i3.p4, not unique enough +-skipping training candidate: hrg_i2.p2, not unique enough +-skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_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_i4.p8, not unique enough -skipping training candidate: Sec16_i4.p9, 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_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough --skipping training candidate: Sec16_i2.p8, not unique enough --skipping training candidate: Sec16_i2.p9, not unique enough +-skipping training candidate: Sec16_i1.p8, not unique enough +-skipping training candidate: Sec16_i1.p9, not unique enough +-skipping training candidate: Sec16_i3.p7, not unique enough +-skipping training candidate: Sec16_i3.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_i2.p3, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i4.p4, not unique enough --skipping training candidate: CanB2_i2.p2, not unique enough --skipping training candidate: IP3K1_i1.p3, not unique enough +-skipping training candidate: CanB2_i1.p2, not unique enough +-skipping training candidate: IP3K1_i2.p2, 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_i2.p8, not unique enough +-skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i3.p5, not unique enough --skipping training candidate: Klp10A_i5.p5, not unique enough --skipping training candidate: Klp10A_i4.p5, not unique enough --skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough +-skipping training candidate: Cdep_i2.p10, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough --skipping training candidate: Cdep_i4.p4, not unique enough --skipping training candidate: Est-6_i2.p2, not unique enough +-skipping training candidate: Est-6_i1.p2, 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_i2.p9, not unique enough +-skipping training candidate: Klp10A_i6.p6, not unique enough -skipping training candidate: Klp10A_i3.p6, not unique enough --skipping training candidate: Klp10A_i5.p6, not unique enough --skipping training candidate: Klp10A_i4.p6, not unique enough --skipping training candidate: Klp10A_i1.p7, not unique enough -skipping training candidate: l(3)05822_i3.p5, 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_i3.p5, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Cnx99A_i2.p5, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough --skipping training candidate: Myo61F_i1.p3, not unique enough +-skipping training candidate: Cnx99A_i3.p5, not unique enough +-skipping training candidate: Myo61F_i4.p3, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough --skipping training candidate: Myo61F_i1.p4, not unique enough +-skipping training candidate: Myo61F_i3.p3, not unique enough +-skipping training candidate: Myo61F_i4.p4, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough --skipping training candidate: bic_i2.p2, 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: CG32082_i2.p4, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough -skipping training candidate: CG32082_i1.p4, not unique enough --skipping training candidate: CG32082_i2.p4, not unique enough --skipping training candidate: Eno_i3.p5, not unique enough --skipping training candidate: Eno_i5.p6, not unique enough +-skipping training candidate: Eno_i6.p5, not unique enough -skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: Eno_i5.p6, not unique enough -skipping training candidate: Eno_i1.p6, not unique enough --skipping training candidate: Sec16_i3.p9, not unique enough --skipping training candidate: Sec16_i1.p10, not unique enough +-skipping training candidate: Eno_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p10, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough +-skipping training candidate: Sec16_i1.p10, not unique enough +-skipping training candidate: Sec16_i3.p9, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i5.p5, not unique enough -skipping training candidate: Dgk_i2.p8, not unique enough --skipping training candidate: nmo_i4.p3, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Dgk_i5.p5, not unique enough +-skipping training candidate: nmo_i6.p3, not unique enough -skipping training candidate: CG33970_i2.p5, not unique enough --skipping training candidate: sqd_i3.p2, not unique enough +-skipping training candidate: sqd_i5.p3, 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_i3.p1, not unique enough +-skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: His4r_i1.p1, not unique enough --skipping training candidate: Hsc70-1_i2.p5, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: Hsc70-1_i3.p4, not unique enough --skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: hrg_i4.p6, not unique enough +-skipping training candidate: hrg_i3.p5, not unique enough -skipping training candidate: CG8136_i3.p2, not unique enough --skipping training candidate: CG8136_i2.p2, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough --skipping training candidate: Myo61F_i1.p5, not unique enough +-skipping training candidate: Myo61F_i4.p5, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough --skipping training candidate: CG6091_i3.p5, not unique enough +-skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i4.p5, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough --skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: CG6145_i5.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_i1.p5, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough +-skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: gukh_i2.p3, not unique enough +-skipping training candidate: sqd_i5.p4, not unique enough +-skipping training candidate: CG33125_i1.p4, not unique enough +-skipping training candidate: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Fri Feb 28 08:50:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.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 +* [Fri Apr 3 17:22:28 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/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 -* [Fri Feb 28 08:50:58 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 -* [Fri Feb 28 08:50:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 08:51:05 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 +* [Fri Apr 3 17:22:29 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 +* [Fri Apr 3 17:22:29 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 +* [Fri Apr 3 17:22:36 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/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 -* [Fri Feb 28 08:51:06 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* [Fri Feb 28 08:51:06 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 -* [Fri Feb 28 08:51:06 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 +* [Fri Apr 3 17:22:36 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/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* [Fri Apr 3 17:22:36 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/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 +* [Fri Apr 3 17:22:37 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 -* [Fri Feb 28 08:51:30 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 +* [Fri Apr 3 17:23:01 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 -* [Fri Feb 28 08:51:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Fri Apr 3 17:23:07 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 -* [Fri Feb 28 08:51:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Fri Apr 3 17:23:08 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 -* [Fri Feb 28 08:51:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Fri Apr 3 17:23:09 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 -* [Fri Feb 28 08:51:39 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 || : +* [Fri Apr 3 17:23:10 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 -* [Fri Feb 28 08:51:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Fri Apr 3 17:23:10 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: -1.16554752737659 instead of -3.29670477662329 --feature swap of score: -1.46290532092963 instead of -3.27511017211415 --feature swap of score: -1.87903690550908 instead of -2.82319503308905 --feature swap of score: -1.50065740976285 instead of -1.76640023701027 --feature swap of score: -0.710016364250829 instead of -1.47751672098809 --feature swap of score: -0.937780180549422 instead of -1.27642853359877 --feature swap of score: 2.02114063616205 instead of -1.20173755595207 --feature swap of score: -0.474123647593194 instead of -1.17627922050008 --feature swap of score: 2.76019576548423 instead of -1.01406213576336 --feature swap of score: -0.516735041108423 instead of -2.45410543731895 --feature swap of score: 2.54037753035113 instead of -1.08138241281938 --feature swap of score: -1.14218452520033 instead of -1.26839705736528 --feature swap of score: -0.878290672115908 instead of -1.51457064124359 --feature swap of score: 0.017266761263424 instead of -1.11486578224486 --feature swap of score: 1.53038492274942 instead of -0.977562781155433 --feature swap of score: 2.13900872551768 instead of -1.23821359149311 --feature swap of score: -1.1749401796647 instead of -1.22789464569142 --feature swap of score: -0.0484872141039334 instead of -1.14950333678695 --feature swap of score: -0.603932745060119 instead of -1.02179906714489 --feature swap of score: -0.00402148723391793 instead of -0.998950293259678 --feature swap of score: -0.0266498286122219 instead of -0.886474550425689 --feature swap of score: 0.654095427322466 instead of -0.701524715903834 --feature swap of score: 3.48883081260896 instead of -0.448256575075822 --feature swap of score: 0.934967637836498 instead of -0.831482619503468 --feature swap of score: -0.664662162790597 instead of -0.786213990501276 --feature swap of score: 2.53996687273351 instead of -0.73973641857243 --feature swap of score: -0.779838274758476 instead of -0.798118188710151 --feature swap of score: -0.183154172767378 instead of -0.277714117151601 --feature swap of score: 1.20167470983539 instead of 0.153943612767378 --feature swap of score: 2.07386584357793 instead of 0.219154117312657 --feature swap of score: 2.41911450351342 instead of -0.231271000589544 --feature swap of score: 0.755071525323755 instead of -0.229114037108175 --feature swap of score: -0.24820928638532 instead of -0.291056626304357 --feature swap of score: 0.427740564602135 instead of -0.428019847107973 --feature swap of score: 0.352944015737907 instead of -0.455713494787044 --feature swap of score: 1.41104743973331 instead of -0.54554556954809 --feature swap of score: -0.0153441105517836 instead of -0.688599173805584 --feature swap of score: 0.940109594386893 instead of -0.337224398103932 --feature swap of score: 2.61369964429552 instead of -0.556879581502916 --feature swap of score: 1.03746660627288 instead of -0.490537024925769 --feature swap of score: 2.2687124540957 instead of -0.30962735850783 --feature swap of score: 0.355966554272142 instead of -0.107762402418587 --feature swap of score: 0.327361078297998 instead of -0.0646294456523155 --feature swap of score: 1.70807813345022 instead of 0.112367133699054 --feature swap of score: 1.82656663058486 instead of -0.00105718155254009 --feature swap of score: 0.89644523788149 instead of 0.195176659988043 --feature swap of score: 0.482495938546138 instead of 0.0940792556532139 --feature swap of score: 3.15621038767898 instead of -0.110852741269907 --feature swap of score: 1.61221062820749 instead of 0.28457476150266 --feature swap of score: 3.44548423884136 instead of 0.494249278314023 --feature swap of score: 1.59831353920368 instead of 0.49471588187656 --feature swap of score: 1.81125355437691 instead of 0.798967685364026 --feature swap of score: 4.76482671982231 instead of 0.55316822454195 --feature swap of score: 0.972453494978998 instead of 0.646514024375041 --feature swap of score: 5.9520466768729 instead of 0.541273583726061 --feature swap of score: 3.55690029692717 instead of 0.354649436973684 --num feature swaps: 56 -* [Fri Feb 28 08:51:40 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: -1.42079898279963 instead of -3.68810504170345 +-feature swap of score: -1.44681537052508 instead of -3.41150532400212 +-feature swap of score: -1.65289098794164 instead of -3.01792121134285 +-feature swap of score: -1.17112151248307 instead of -1.39916906554853 +-feature swap of score: -0.75975902139825 instead of -1.21594572877466 +-feature swap of score: 1.97531481073561 instead of -1.09350712313481 +-feature swap of score: -0.525229632905267 instead of -0.955754554553279 +-feature swap of score: 2.86027054787895 instead of -0.957728902499315 +-feature swap of score: -0.535645609682768 instead of -0.965401379771999 +-feature swap of score: 2.17673024476124 instead of -1.12779544014257 +-feature swap of score: -0.66872364518718 instead of -0.873580236571325 +-feature swap of score: 0.104972736949564 instead of -0.741270035654323 +-feature swap of score: 1.13978375718415 instead of -0.90065217598589 +-feature swap of score: 1.82314707438642 instead of -1.18455419364355 +-feature swap of score: 0.571564808042379 instead of -1.20660957072496 +-feature swap of score: -0.779423611664128 instead of -1.16324574338006 +-feature swap of score: 0.641980495280439 instead of -0.957051565915332 +-feature swap of score: -0.379020470105372 instead of -0.889079770795895 +-feature swap of score: 1.2262672023959 instead of -1.03516080863888 +-feature swap of score: 2.46802814838397 instead of -0.76958414839795 +-feature swap of score: 1.19691979248836 instead of -2.38211004793244 +-feature swap of score: 0.247861590824157 instead of -0.855562578459738 +-feature swap of score: 0.0414216348225098 instead of -0.863083862369428 +-feature swap of score: 2.6928673026898 instead of -0.604907692499259 +-feature swap of score: -0.259410279403675 instead of -0.837622887705597 +-feature swap of score: -0.435141257808462 instead of -0.560642365197203 +-feature swap of score: 0.118859238819426 instead of -0.59295940972102 +-feature swap of score: 2.66002527902716 instead of -0.858025497689884 +-feature swap of score: 1.19858076591114 instead of -0.286134619573751 +-feature swap of score: 2.56505502974622 instead of -0.325650608818922 +-feature swap of score: -0.0233179027872717 instead of -0.243250015591876 +-feature swap of score: 2.73914080505453 instead of -0.23285323748664 +-feature swap of score: 0.226161148598426 instead of -0.600548704935031 +-feature swap of score: 1.57060255118184 instead of -0.952015480939538 +-feature swap of score: 0.185912000179283 instead of -0.336260737370033 +-feature swap of score: 0.645108971733555 instead of -0.515816978105198 +-feature swap of score: 0.750144899137576 instead of -0.600590671855687 +-feature swap of score: 0.674940397348908 instead of -0.358808301986617 +-feature swap of score: 2.35968732178866 instead of -0.128527843957486 +-feature swap of score: 0.567163520730274 instead of -0.0365513796211537 +-feature swap of score: 1.76020692491126 instead of 0.173521414513822 +-feature swap of score: 0.327325652172758 instead of -0.0266365563631694 +-feature swap of score: 0.116932100459094 instead of 0.0857233490009411 +-feature swap of score: 0.939122171502681 instead of -0.143858806299319 +-feature swap of score: 0.452615735719004 instead of 0.179053641822607 +-feature swap of score: 1.40809878292928 instead of 0.48136445889912 +-feature swap of score: 2.96569904924868 instead of 0.556882774870917 +-feature swap of score: 0.721939006704945 instead of 0.480911815417957 +-feature swap of score: 0.672377175271524 instead of 0.464143602465669 +-feature swap of score: 2.05815954399679 instead of 0.386721524712429 +-feature swap of score: 2.42654214228993 instead of 0.445114224136472 +-feature swap of score: 1.94542319643394 instead of 0.815869959201074 +-feature swap of score: 0.456402568510292 instead of 0.323244567451772 +-feature swap of score: 1.10756639129077 instead of 0.13789786297723 +-feature swap of score: 7.61143554593931 instead of 0.265049354450872 +-feature swap of score: 1.95562377154162 instead of 0.739789815933576 +-feature swap of score: 2.98587126378045 instead of 0.817172488846074 +-feature swap of score: 8.91817104434026 instead of 0.714523149516384 +-feature swap of score: 1.91775494466018 instead of 0.588817198471288 +-num feature swaps: 59 +* [Fri Apr 3 17:23:11 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 -* [Fri Feb 28 08:52:02 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/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 +* [Fri Apr 3 17:23:34 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 -* [Fri Feb 28 08:52:08 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 || : +* [Fri Apr 3 17:23:40 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 -* [Fri Feb 28 08:52:09 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 +* [Fri Apr 3 17:23:41 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 -* [Fri Feb 28 08:52:11 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 || : +* [Fri Apr 3 17:23:42 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 -* [Fri Feb 28 08:52:11 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 +* [Fri Apr 3 17:23:42 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: 15 -* [Fri Feb 28 08:52:11 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* [Fri Feb 28 08:52:11 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: 17 +* [Fri Apr 3 17:23:43 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* [Fri Apr 3 17:23:43 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 -* [Fri Feb 28 08:52:12 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 +* [Fri Apr 3 17:23:43 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 -* [Fri Feb 28 08:52:12 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 +* [Fri Apr 3 17:23:43 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.* @@ -13673,9 +13712,9 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. --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.p7. +-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.p2. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. @@ -13816,12 +13855,14 @@ 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/352007/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/352007/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/3680447 and its subdirectories -I: Current time: Fri Feb 28 08:52:32 -12 2025 -I: pbuilder-time-stamp: 1740775952 +I: removing directory /srv/workspace/pbuilder/352007 and its subdirectories +I: Current time: Fri Apr 3 17:24:04 +14 2026 +I: pbuilder-time-stamp: 1775186644