Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 21:01:37.133031016 +0000 +++ b2/build.log 2024-05-13 21:10:02.627539485 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 15 15:16:13 -12 2025 -I: pbuilder-time-stamp: 1750043773 +I: Current time: Tue May 14 11:01:41 +14 2024 +I: pbuilder-time-stamp: 1715634101 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1546464/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3914991/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-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 May 13 21:01 /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/3914991/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3914991/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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='919ffdf9e70742bd9704ce2bdfdc5726' - 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='1546464' - PS1='# ' - PS2='> ' + INVOCATION_ID=2a1282850c3545e1a285db72f1994b20 + 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=3914991 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.jucxNzvZ/pbuilderrc_56C6 --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.jucxNzvZ/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.jucxNzvZ/pbuilderrc_xqxM --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.jucxNzvZ/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 codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 15 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1546464/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 11:38 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3914991/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -277,7 +309,7 @@ Get: 153 http://deb.debian.org/debian trixie/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [420 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] -Fetched 119 MB in 1s (160 MB/s) +Fetched 119 MB in 1s (232 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19744 files and directories currently installed.) @@ -796,8 +828,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 16 03:16:41 UTC 2025. -Universal Time is now: Mon Jun 16 03:16:41 UTC 2025. +Local time is now: Mon May 13 21:02:09 UTC 2024. +Universal Time is now: Mon May 13 21:02:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -945,7 +977,11 @@ 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/3914991/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3914991/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 @@ -1009,7 +1045,7 @@ ## 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 -* [Sun Jun 15 15:16:56 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/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue May 14 11:02:29 2024] 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. @@ -1061,13 +1097,13 @@ fi -Building a new DB, current time: 06/15/2025 15:16:56 +Building a new DB, current time: 05/14/2024 11:02:30 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: 1000000000B -Adding sequences from FASTA; added 240 sequences in 0.009377 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00929523 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1142,8 +1178,8 @@ 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: 947.48 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1666.05 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1200,8 +1236,8 @@ 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: 909.62 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 846.82 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1265,8 +1301,8 @@ 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: 1168.12 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1605.33 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1327,7 +1363,7 @@ 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: 1023.32 +# Mc/sec: 986.83 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1387,8 +1423,8 @@ 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: 332.33 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 320.44 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1438,8 +1474,8 @@ 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: 262.08 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 264.48 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1503,8 +1539,8 @@ 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: 1131.96 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1059.36 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1557,7 +1593,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 280.25 +# Mc/sec: 276.31 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1608,7 +1644,7 @@ 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: 910.86 +# Mc/sec: 956.09 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1664,8 +1700,8 @@ 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: 1050.72 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1045.78 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1754,7 +1790,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 741.90 +# Mc/sec: 726.12 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1838,8 +1874,8 @@ 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: 835.67 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 834.95 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1895,8 +1931,8 @@ 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 457.02 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 450.13 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1952,8 +1988,8 @@ 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 458.85 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 457.77 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2010,7 +2046,7 @@ 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: 1327.20 +# Mc/sec: 1354.38 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2055,7 +2091,7 @@ 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: 1088.38 +# Mc/sec: 1099.72 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2108,7 +2144,7 @@ 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: 1387.09 +# Mc/sec: 1269.65 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2153,7 +2189,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 884.28 +# Mc/sec: 891.55 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2214,7 +2250,7 @@ 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: 666.34 +# Mc/sec: 680.16 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2265,7 +2301,7 @@ 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: 615.19 +# Mc/sec: 625.78 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2377,8 +2413,8 @@ 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 504.75 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 498.87 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2425,7 +2461,7 @@ 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: 1056.31 +# Mc/sec: 1041.65 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2492,7 +2528,7 @@ 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: 968.76 +# Mc/sec: 960.08 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2531,7 +2567,7 @@ 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: 1819.15 +# Mc/sec: 1831.25 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2607,8 +2643,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 761.11 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 766.12 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2660,8 +2696,8 @@ 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: 1133.85 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1175.66 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2746,7 +2782,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 219.62 +# Mc/sec: 217.65 // Query: DLH [M=217] Accession: PF01738.17 @@ -2794,7 +2830,7 @@ 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: 1534.96 +# Mc/sec: 1535.58 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2841,7 +2877,7 @@ 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: 981.82 +# Mc/sec: 963.22 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2891,7 +2927,7 @@ 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: 1302.23 +# Mc/sec: 1287.80 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2933,8 +2969,8 @@ 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: 1534.47 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1555.24 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -2979,8 +3015,8 @@ 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: 580.42 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 579.90 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3018,7 +3054,7 @@ 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: 1420.15 +# Mc/sec: 1417.86 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3069,8 +3105,8 @@ 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: 708.89 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 697.64 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3108,7 +3144,7 @@ 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: 776.65 +# Mc/sec: 819.25 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3146,7 +3182,7 @@ 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: 1533.98 +# Mc/sec: 1496.49 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3196,8 +3232,8 @@ 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: 1029.35 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1039.37 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3234,8 +3270,8 @@ 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: 1949.90 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1924.23 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3295,8 +3331,8 @@ 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: 1076.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1060.23 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3340,8 +3376,8 @@ 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: 1088.90 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1102.91 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3397,8 +3433,8 @@ 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: 1077.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1037.14 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3453,7 +3489,7 @@ 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: 398.39 +# Mc/sec: 397.34 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3490,8 +3526,8 @@ 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: 1800.97 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1740.03 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3567,8 +3603,8 @@ 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: 1163.83 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1151.27 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3632,8 +3668,8 @@ 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: 343.28 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 340.28 // Query: FPP [M=866] Accession: PF05911.10 @@ -3683,8 +3719,8 @@ 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 1060.19 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 1047.51 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3737,7 +3773,7 @@ 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: 1120.45 +# Mc/sec: 1150.21 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3861,7 +3897,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 300.52 +# Mc/sec: 302.80 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3900,7 +3936,7 @@ 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: 833.29 +# Mc/sec: 823.89 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -3990,8 +4026,8 @@ 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 391.32 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 385.07 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4041,8 +4077,8 @@ 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: 302.14 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 257.51 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4102,8 +4138,8 @@ 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: 730.19 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 725.01 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4207,8 +4243,8 @@ 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 389.77 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 389.79 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4256,7 +4292,7 @@ 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: 1195.32 +# Mc/sec: 1185.75 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4331,7 +4367,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 618.48 +# Mc/sec: 621.42 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4402,7 +4438,7 @@ 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: 910.08 +# Mc/sec: 922.10 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4450,7 +4486,7 @@ 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: 463.68 +# Mc/sec: 458.76 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4520,8 +4556,8 @@ 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 -# Mc/sec: 154.35 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 152.70 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4571,8 +4607,8 @@ 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: 1517.68 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1451.53 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4622,8 +4658,8 @@ 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: 1648.56 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1571.19 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4662,7 +4698,7 @@ 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: 1099.69 +# Mc/sec: 1087.93 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4706,8 +4742,8 @@ 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: 1003.66 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1001.89 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4759,7 +4795,7 @@ 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: 823.70 +# Mc/sec: 768.98 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4841,8 +4877,8 @@ 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: 544.33 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 541.97 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4942,8 +4978,8 @@ 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 423.22 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 413.61 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -4997,8 +5033,8 @@ 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: 692.78 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 699.36 // Query: IBR [M=62] Accession: PF01485.20 @@ -5035,8 +5071,8 @@ 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: 894.65 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 914.02 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5083,8 +5119,8 @@ 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: 527.95 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 533.31 // Query: malic [M=182] Accession: PF00390.18 @@ -5122,8 +5158,8 @@ 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: 2046.52 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2095.99 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5161,7 +5197,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 587.68 +# Mc/sec: 595.08 // Query: MatE [M=161] Accession: PF01554.17 @@ -5245,8 +5281,8 @@ 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: 685.58 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 688.45 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5284,7 +5320,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1621.38 +# Mc/sec: 1585.56 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5458,8 +5494,8 @@ 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: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.07 -# Mc/sec: 138.77 +# CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.08 +# Mc/sec: 136.84 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5501,8 +5537,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 1149.84 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1684.85 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5559,7 +5595,7 @@ 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: 591.40 +# Mc/sec: 585.33 // Query: MIP [M=227] Accession: PF00230.19 @@ -5609,8 +5645,8 @@ 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: 1272.92 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1261.34 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5662,8 +5698,8 @@ 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: 703.73 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 692.82 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5754,7 +5790,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1037.74 +# Mc/sec: 1031.55 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5791,8 +5827,8 @@ 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: 1028.25 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 986.06 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5829,8 +5865,8 @@ 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: 1571.34 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1591.97 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5883,7 +5919,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1249.40 +# Mc/sec: 1224.22 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5920,8 +5956,8 @@ 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: 1793.22 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1803.77 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6042,7 +6078,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 553.75 +# Mc/sec: 552.68 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6092,8 +6128,8 @@ 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: 1353.51 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1337.60 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6163,8 +6199,8 @@ 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: 1036.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1053.01 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6217,7 +6253,7 @@ 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: 00:00:00.02 -# Mc/sec: 505.63 +# Mc/sec: 494.01 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6279,8 +6315,8 @@ 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: 941.72 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 920.06 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6383,7 +6419,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 134.71 +# Mc/sec: 134.49 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6430,8 +6466,8 @@ 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: 1241.23 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1231.68 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6482,7 +6518,7 @@ 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: 739.07 +# Mc/sec: 734.24 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6532,8 +6568,8 @@ 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: 1089.92 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1058.00 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6583,8 +6619,8 @@ 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: 1508.75 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1484.53 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6629,7 +6665,7 @@ 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: 1606.23 +# Mc/sec: 1526.62 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6675,8 +6711,8 @@ 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: 672.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 753.51 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6740,8 +6776,8 @@ 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: 291.67 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 287.80 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6786,7 +6822,7 @@ 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: 1053.68 +# Mc/sec: 902.08 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6839,7 +6875,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 486.30 +# Mc/sec: 478.16 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6884,7 +6920,7 @@ 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: 1619.50 +# Mc/sec: 1554.79 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -6985,7 +7021,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 -# Mc/sec: 309.67 +# Mc/sec: 302.96 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7030,7 +7066,7 @@ 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: 383.53 +# Mc/sec: 372.71 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7083,7 +7119,7 @@ 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: 1258.23 +# Mc/sec: 1090.59 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7156,8 +7192,8 @@ 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 208.78 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 201.85 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7218,7 +7254,7 @@ 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: 1111.81 +# Mc/sec: 1090.40 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7262,8 +7298,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1170.89 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1122.93 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7315,8 +7351,8 @@ 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: 1144.37 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1127.97 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7354,7 +7390,7 @@ 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: 2694.02 +# Mc/sec: 2738.20 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7396,8 +7432,8 @@ 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: 1494.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1503.18 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7459,8 +7495,8 @@ 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 -# Mc/sec: 399.63 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 415.99 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7497,8 +7533,8 @@ 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: 1642.28 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1645.68 // Query: Usher [M=551] Accession: PF00577.19 @@ -7542,8 +7578,8 @@ 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: 1430.46 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1395.98 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7590,7 +7626,7 @@ 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: 453.85 +# Mc/sec: 445.54 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7635,7 +7671,7 @@ 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: 459.43 +# Mc/sec: 451.83 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7679,8 +7715,8 @@ 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: 485.68 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 486.25 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7735,7 +7771,7 @@ 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: 544.84 +# Mc/sec: 523.87 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7773,8 +7809,8 @@ 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: 310.95 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 309.43 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7826,7 +7862,7 @@ 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: 517.55 +# Mc/sec: 462.52 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7874,7 +7910,7 @@ 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: 765.08 +# Mc/sec: 723.71 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7912,15 +7948,15 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 693.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 627.87 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Sun Jun 15 15:16:58 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/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 -* [Sun Jun 15 15:16:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue May 14 11:02:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue May 14 11:02:32 2024] 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 @@ -7947,39 +7983,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Sun Jun 15 15:16:58 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/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue May 14 11:02:32 2024] 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 -* [Sun Jun 15 15:16:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Sun Jun 15 15:16:59 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/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 -* [Sun Jun 15 15:17:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue May 14 11:02:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Tue May 14 11:02:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue May 14 11:02:33 2024] 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... -* [Sun Jun 15 15:17:00 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* [Sun Jun 15 15:17:00 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 -* [Sun Jun 15 15:17:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue May 14 11:02:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue May 14 11:02:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue May 14 11:02:34 2024] 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 -* [Sun Jun 15 15:17:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:02:49 2024] 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 -* [Sun Jun 15 15:17:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue May 14 11:02:53 2024] 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 -* [Sun Jun 15 15:17:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:02:54 2024] 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 -* [Sun Jun 15 15:17:22 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue May 14 11:02:56 2024] 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 -* [Sun Jun 15 15:17:22 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue May 14 11:02:56 2024] 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 -* [Sun Jun 15 15:17:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue May 14 11:02:57 2024] 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 @@ -7989,33 +8025,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Sun Jun 15 15:17:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue May 14 11:02:57 2024] 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 -* [Sun Jun 15 15:17:39 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 +* [Tue May 14 11:03:13 2024] 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 -* [Sun Jun 15 15:17:43 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 || : +* [Tue May 14 11:03:17 2024] 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 -* [Sun Jun 15 15:17:44 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 +* [Tue May 14 11:03:18 2024] 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 -* [Sun Jun 15 15:17:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue May 14 11:03:19 2024] 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 -* [Sun Jun 15 15:17:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue May 14 11:03:19 2024] 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 -* [Sun Jun 15 15:17:46 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* [Sun Jun 15 15:17:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed +* [Tue May 14 11:03:20 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Tue May 14 11:03:20 2024] 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 -* [Sun Jun 15 15:17:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep +* [Tue May 14 11:03:20 2024] 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 -* [Sun Jun 15 15:17:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds +* [Tue May 14 11:03:20 2024] 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.* @@ -8107,7 +8143,7 @@ ../../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 -* [Sun Jun 15 15:17:47 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 +* [Tue May 14 11:03:21 2024] 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. @@ -8131,8 +8167,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Sun Jun 15 15:17:49 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 -* [Sun Jun 15 15:17:49 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 +* [Tue May 14 11:03:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue May 14 11:03:23 2024] 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 @@ -8807,37 +8843,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Sun Jun 15 15:17:49 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.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue May 14 11:03:23 2024] 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 -* [Sun Jun 15 15:17:50 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 -* [Sun Jun 15 15:17:51 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 -* [Sun Jun 15 15:17:58 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 +* [Tue May 14 11:03:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores +* [Tue May 14 11:03:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue May 14 11:03:32 2024] 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 -* [Sun Jun 15 15:17:58 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* [Sun Jun 15 15:17:58 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 -* [Sun Jun 15 15:17:58 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/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue May 14 11:03:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue May 14 11:03:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue May 14 11:03:32 2024] 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 -* [Sun Jun 15 15:18:23 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 +* [Tue May 14 11:03:56 2024] 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 -* [Sun Jun 15 15:18:29 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 || : +* [Tue May 14 11:04:02 2024] 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 -* [Sun Jun 15 15:18:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:04:04 2024] 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 -* [Sun Jun 15 15:18:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue May 14 11:04:05 2024] 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 -* [Sun Jun 15 15:18:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue May 14 11:04:05 2024] 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 -* [Sun Jun 15 15:18:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue May 14 11:04:06 2024] 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 @@ -8896,33 +8932,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Sun Jun 15 15:18:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue May 14 11:04:06 2024] 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 -* [Sun Jun 15 15:18:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:04:29 2024] 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 -* [Sun Jun 15 15:19:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue May 14 11:04:35 2024] 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 -* [Sun Jun 15 15:19:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:04:36 2024] 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 -* [Sun Jun 15 15:19:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue May 14 11:04:37 2024] 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 -* [Sun Jun 15 15:19:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue May 14 11:04:38 2024] 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 -* [Sun Jun 15 15:19:05 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* [Sun Jun 15 15:19:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed +* [Tue May 14 11:04:38 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Tue May 14 11:04:38 2024] 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 -* [Sun Jun 15 15:19:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep +* [Tue May 14 11:04:38 2024] 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 -* [Sun Jun 15 15:19:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds +* [Tue May 14 11:04:39 2024] 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.* @@ -8979,8 +9015,8 @@ 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.p3. --Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. +-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 [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 @@ -9015,7 +9051,7 @@ 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 -* [Sun Jun 15 15:19:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat +* [Tue May 14 11:04:40 2024] 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. @@ -9035,8 +9071,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Sun Jun 15 15:19:09 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 -* [Sun Jun 15 15:19:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue May 14 11:04:42 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue May 14 11:04:42 2024] 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 @@ -9074,37 +9110,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Sun Jun 15 15:19:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue May 14 11:04:43 2024] 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 -* [Sun Jun 15 15:19:10 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 -* [Sun Jun 15 15:19:12 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 -* [Sun Jun 15 15:19:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue May 14 11:04:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores +* [Tue May 14 11:04:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue May 14 11:04:52 2024] 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 -* [Sun Jun 15 15:19:20 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* [Sun Jun 15 15:19:20 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 -* [Sun Jun 15 15:19:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue May 14 11:04:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue May 14 11:04:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue May 14 11:04:53 2024] 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 -* [Sun Jun 15 15:19:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:05:18 2024] 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 -* [Sun Jun 15 15:19:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue May 14 11:05:24 2024] 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 -* [Sun Jun 15 15:19:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:05:25 2024] 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 -* [Sun Jun 15 15:19:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue May 14 11:05:26 2024] 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 -* [Sun Jun 15 15:19:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue May 14 11:05:27 2024] 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 -* [Sun Jun 15 15:19:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue May 14 11:05:28 2024] 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 @@ -9210,33 +9246,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Sun Jun 15 15:19:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue May 14 11:05:28 2024] 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 -* [Sun Jun 15 15:20:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:05:52 2024] 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 -* [Sun Jun 15 15:20:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue May 14 11:05:58 2024] 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 -* [Sun Jun 15 15:20:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:05:59 2024] 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 -* [Sun Jun 15 15:20:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue May 14 11:06:00 2024] 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 -* [Sun Jun 15 15:20:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue May 14 11:06:01 2024] 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 -* [Sun Jun 15 15:20:28 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* [Sun Jun 15 15:20:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed +* [Tue May 14 11:06:01 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Tue May 14 11:06:01 2024] 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 -* [Sun Jun 15 15:20:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep +* [Tue May 14 11:06:01 2024] 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 -* [Sun Jun 15 15:20:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds +* [Tue May 14 11:06:01 2024] 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.* @@ -9253,32 +9289,32 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'contig' => 'III', + 'trans_id' => '', + 'asmbl' => 'comp1051_c1_seq1', + 'orient' => '-', 'coords' => [ [ '1642973', '1644586' ] ], - 'trans_id' => '', - 'asmbl' => 'comp1051_c1_seq1', - 'orient' => '-' + 'gene_id' => '' }; - gene_length: 1616 - num_exons: 1 - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 - Model_feat_name: comp1051_c1_seq1.p1 - gene_type: protein-coding strand: + - source: transdecoder - mid_pt: 808 is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=83.26 asmbl_id: comp1051_c1_seq1 + num_exons: 1 classification: annotated_genes - is_5prime_partial: 0 + gene_length: 1616 is_pseudogene: 0 + is_5prime_partial: 0 + mid_pt: 808 + Model_feat_name: comp1051_c1_seq1.p1 + gene_type: protein-coding + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + com_name: ORF type:5prime_partial (+),score=83.26 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9295,11 +9331,7 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp1058_c0_seq1', - 'orient' => '-', 'gene_id' => '', - 'contig' => 'I', - 'trans_id' => '', 'coords' => [ [ 5095548, @@ -9309,22 +9341,26 @@ 5095142, '5095301' ] - ] + ], + 'orient' => '-', + 'asmbl' => 'comp1058_c0_seq1', + 'trans_id' => '', + 'contig' => 'I' }; - is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=32.57 - strand: + + gene_type: protein-coding + Model_feat_name: comp1058_c0_seq1.p1 source: transdecoder + com_name: ORF type:5prime_partial (+),score=32.57 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + gene_length: 496 + is_5prime_partial: 0 mid_pt: 248 is_pseudogene: 0 - is_5prime_partial: 0 - classification: annotated_genes - asmbl_id: comp1058_c0_seq1 - gene_length: 496 - gene_type: protein-coding num_exons: 1 - Model_feat_name: comp1058_c0_seq1.p1 - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + asmbl_id: comp1058_c0_seq1 + classification: annotated_genes + strand: + + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9347,8 +9383,6 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'asmbl' => 'comp1112_c0_seq1', 'coords' => [ [ 2380416, @@ -9359,24 +9393,26 @@ '2380336' ] ], - 'trans_id' => '', + 'orient' => '-', + 'gene_id' => '', 'contig' => 'III', - 'gene_id' => '' + 'asmbl' => 'comp1112_c0_seq1', + 'trans_id' => '' }; - gene_length: 2081 + classification: annotated_genes + asmbl_id: comp1112_c0_seq1 num_exons: 1 + is_3prime_partial: 0 + strand: + + source: transdecoder + com_name: ORF type:complete (+),score=155.28 TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 - Model_feat_name: comp1112_c0_seq1.p1 gene_type: protein-coding - source: transdecoder - strand: + + Model_feat_name: comp1112_c0_seq1.p1 mid_pt: 1041 - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=155.28 - asmbl_id: comp1112_c0_seq1 - classification: annotated_genes is_5prime_partial: 0 is_pseudogene: 0 + gene_length: 2081 gene_synonyms: mRNA_coords CDS_coords @@ -9398,10 +9434,9 @@ -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', - 'orient' => '-', - 'gene_id' => '', 'contig' => 'II', + 'asmbl' => 'comp1198_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 402195, @@ -9420,22 +9455,23 @@ '401683' ] ], - 'trans_id' => '' + 'orient' => '-', + 'gene_id' => '' }; - asmbl_id: comp1198_c0_seq1 - classification: annotated_genes + mid_pt: 299 is_5prime_partial: 0 is_pseudogene: 0 - mid_pt: 299 + gene_length: 597 source: transdecoder - strand: + com_name: ORF type:internal (+),score=37.56 - is_3prime_partial: 0 - Model_feat_name: comp1198_c0_seq1.p1 TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - num_exons: 1 gene_type: protein-coding - gene_length: 597 + Model_feat_name: comp1198_c0_seq1.p1 + is_3prime_partial: 0 + strand: + + classification: annotated_genes + num_exons: 1 + asmbl_id: comp1198_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9463,6 +9499,9 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'contig' => 'III', + 'asmbl' => 'comp1210_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 368840, @@ -9473,26 +9512,23 @@ '368790' ] ], - 'trans_id' => '', - 'contig' => 'III', - 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp1210_c0_seq1' + 'gene_id' => '' }; - num_exons: 1 - Model_feat_name: comp1210_c0_seq1.p1 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 - gene_type: protein-coding - gene_length: 1554 - asmbl_id: comp1210_c0_seq1 + is_3prime_partial: 0 + strand: + classification: annotated_genes + asmbl_id: comp1210_c0_seq1 + num_exons: 1 is_pseudogene: 0 + mid_pt: 777 is_5prime_partial: 0 + gene_length: 1554 + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 source: transdecoder - strand: + - mid_pt: 777 - is_3prime_partial: 0 com_name: ORF type:5prime_partial (+),score=12.16 + Model_feat_name: comp1210_c0_seq1.p1 + gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9517,8 +9553,8 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp366_c0_seq1', 'coords' => [ [ '3840968', @@ -9526,23 +9562,23 @@ ] ], 'trans_id' => '', - 'contig' => 'II', - 'gene_id' => '' + 'asmbl' => 'comp366_c0_seq1', + 'contig' => 'II' }; - gene_type: protein-coding + is_3prime_partial: 0 + strand: - + classification: annotated_genes num_exons: 1 - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - Model_feat_name: comp366_c0_seq1.p1 - gene_length: 340 + asmbl_id: comp366_c0_seq1 is_pseudogene: 0 + mid_pt: 170 is_5prime_partial: 0 - classification: annotated_genes - asmbl_id: comp366_c0_seq1 - is_3prime_partial: 0 + gene_length: 340 + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 com_name: ORF type:internal (-),score=12.83 - strand: - source: transdecoder - mid_pt: 170 + Model_feat_name: comp366_c0_seq1.p1 + gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9568,30 +9604,30 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'contig' => 'I', + 'asmbl' => 'comp610_c0_seq1', + 'trans_id' => '', 'coords' => [ [ '5471264', '5472770' ] ], - 'trans_id' => '', - 'contig' => 'I', 'orient' => '-', - 'asmbl' => 'comp610_c0_seq1' + 'gene_id' => '' }; - gene_length: 1509 - gene_type: protein-coding num_exons: 1 - Model_feat_name: comp610_c0_seq1.p1 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=50.55 + asmbl_id: comp610_c0_seq1 + classification: annotated_genes strand: + + is_3prime_partial: 0 + gene_type: protein-coding + Model_feat_name: comp610_c0_seq1.p1 source: transdecoder + com_name: ORF type:5prime_partial (+),score=50.55 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + gene_length: 1509 mid_pt: 755 - classification: annotated_genes - asmbl_id: comp610_c0_seq1 is_5prime_partial: 0 is_pseudogene: 0 gene_synonyms: @@ -9612,31 +9648,31 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], - 'trans_id' => '', - 'contig' => 'I', 'orient' => '-', - 'asmbl' => 'comp645_c0_seq1' + 'gene_id' => '', + 'contig' => 'I', + 'asmbl' => 'comp645_c0_seq1', + 'trans_id' => '' }; - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 Model_feat_name: comp645_c0_seq1.p1 - num_exons: 1 gene_type: protein-coding + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=273.35 + source: transdecoder gene_length: 3653 - asmbl_id: comp645_c0_seq1 - classification: annotated_genes is_pseudogene: 0 is_5prime_partial: 0 mid_pt: 1827 - source: transdecoder + asmbl_id: comp645_c0_seq1 + num_exons: 1 + classification: annotated_genes strand: + - com_name: ORF type:5prime_partial (+),score=273.35 is_3prime_partial: 0 gene_synonyms: mRNA_coords @@ -9654,6 +9690,7 @@ Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'contig' => 'II', + 'asmbl' => 'comp688_c0_seq1', 'trans_id' => '', 'coords' => [ [ @@ -9665,24 +9702,23 @@ '381243' ] ], - 'gene_id' => '', - 'asmbl' => 'comp688_c0_seq1', - 'orient' => '+' + 'orient' => '+', + 'gene_id' => '' }; - strand: + + Model_feat_name: comp688_c0_seq1.p1 + gene_type: protein-coding + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 source: transdecoder - mid_pt: 1392 - is_3prime_partial: 0 com_name: ORF type:complete (+),score=172.54 - is_5prime_partial: 0 + gene_length: 2784 is_pseudogene: 0 + mid_pt: 1392 + is_5prime_partial: 0 + num_exons: 1 asmbl_id: comp688_c0_seq1 classification: annotated_genes - gene_length: 2784 - num_exons: 1 - Model_feat_name: comp688_c0_seq1.p1 - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 - gene_type: protein-coding + strand: + + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9706,10 +9742,6 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '+', - 'asmbl' => 'comp856_c0_seq1', - 'gene_id' => '', - 'trans_id' => '', 'coords' => [ [ 3753910, @@ -9720,22 +9752,26 @@ '3755057' ] ], - 'contig' => 'II' + 'orient' => '+', + 'gene_id' => '', + 'contig' => 'II', + 'asmbl' => 'comp856_c0_seq1', + 'trans_id' => '' }; - is_5prime_partial: 0 is_pseudogene: 0 - classification: annotated_genes - asmbl_id: comp856_c0_seq1 - com_name: ORF type:complete (+),score=71.94 - is_3prime_partial: 0 + is_5prime_partial: 0 mid_pt: 785 - source: transdecoder - strand: + - gene_type: protein-coding + gene_length: 1569 TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + com_name: ORF type:complete (+),score=71.94 + source: transdecoder Model_feat_name: comp856_c0_seq1.p1 + gene_type: protein-coding + is_3prime_partial: 0 + strand: + + classification: annotated_genes + asmbl_id: comp856_c0_seq1 num_exons: 1 - gene_length: 1569 gene_synonyms: mRNA_coords CDS_coords @@ -9755,10 +9791,7 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp873_c0_seq2', 'orient' => '-', - 'contig' => 'II', - 'trans_id' => '', 'coords' => [ [ 3727877, @@ -9773,22 +9806,25 @@ '3727657' ] ], - 'gene_id' => '' + 'gene_id' => '', + 'contig' => 'II', + 'trans_id' => '', + 'asmbl' => 'comp873_c0_seq2' }; + classification: annotated_genes + asmbl_id: comp873_c0_seq2 + num_exons: 1 is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=8.59 strand: + + com_name: ORF type:5prime_partial (+),score=8.59 source: transdecoder - mid_pt: 513 + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + gene_type: protein-coding + Model_feat_name: comp873_c0_seq2.p1 is_5prime_partial: 0 + mid_pt: 513 is_pseudogene: 0 - classification: annotated_genes - asmbl_id: comp873_c0_seq2 gene_length: 1025 - gene_type: protein-coding - num_exons: 1 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 - Model_feat_name: comp873_c0_seq2.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9812,9 +9848,7 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'contig' => 'III', - 'trans_id' => '', + 'orient' => '-', 'coords' => [ [ 1268244, @@ -9825,23 +9859,25 @@ '1268172' ] ], - 'asmbl' => 'comp888_c0_seq1', - 'orient' => '-' + 'gene_id' => '', + 'contig' => 'III', + 'trans_id' => '', + 'asmbl' => 'comp888_c0_seq1' }; + com_name: ORF type:5prime_partial (+),score=23.94 + source: transdecoder + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_type: protein-coding - num_exons: 1 Model_feat_name: comp888_c0_seq1.p1 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 + mid_pt: 295 + is_5prime_partial: 0 + is_pseudogene: 0 gene_length: 589 classification: annotated_genes + num_exons: 1 asmbl_id: comp888_c0_seq1 - is_5prime_partial: 0 - is_pseudogene: 0 is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=23.94 - source: transdecoder strand: + - mid_pt: 295 gene_synonyms: mRNA_coords CDS_coords @@ -9863,10 +9899,6 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp940_c0_seq1', - 'orient' => '+', - 'gene_id' => '', - 'contig' => 'III', 'coords' => [ [ 105641, @@ -9877,21 +9909,25 @@ '106404' ] ], + 'orient' => '+', + 'gene_id' => '', + 'contig' => 'III', + 'asmbl' => 'comp940_c0_seq1', 'trans_id' => '' }; - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=94.37 - source: transdecoder strand: + + is_3prime_partial: 0 + num_exons: 1 + asmbl_id: comp940_c0_seq1 + classification: annotated_genes + gene_length: 2129 mid_pt: 1065 is_5prime_partial: 0 is_pseudogene: 0 - classification: annotated_genes - asmbl_id: comp940_c0_seq1 - gene_length: 2129 gene_type: protein-coding - num_exons: 1 Model_feat_name: comp940_c0_seq1.p1 + source: transdecoder + com_name: ORF type:complete (+),score=94.37 TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 gene_synonyms: mRNA_coords @@ -9912,8 +9948,11 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'trans_id' => '', + 'asmbl' => 'comp983_c0_seq1', 'contig' => 'I', + 'gene_id' => '', + 'orient' => '-', 'coords' => [ [ 4100066, @@ -9923,25 +9962,22 @@ 4098246, '4100014' ] - ], - 'trans_id' => '', - 'asmbl' => 'comp983_c0_seq1', - 'orient' => '-' + ] }; - com_name: ORF type:5prime_partial (+),score=143.65 - is_3prime_partial: 0 - mid_pt: 935 - source: transdecoder strand: + - classification: annotated_genes + is_3prime_partial: 0 + num_exons: 1 asmbl_id: comp983_c0_seq1 - is_pseudogene: 0 - is_5prime_partial: 0 + classification: annotated_genes gene_length: 1870 + is_5prime_partial: 0 + mid_pt: 935 + is_pseudogene: 0 gene_type: protein-coding Model_feat_name: comp983_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=143.65 + source: transdecoder TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 - num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9985,7 +10021,7 @@ ## 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 -* [Sun Jun 15 15:20:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue May 14 11:06:03 2024] 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. @@ -10010,8 +10046,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Sun Jun 15 15:20:45 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 -* [Sun Jun 15 15:20:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue May 14 11:06:16 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue May 14 11:06:17 2024] 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 @@ -12629,37 +12665,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Sun Jun 15 15:20:48 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 +* [Tue May 14 11:06:19 2024] 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 -* [Sun Jun 15 15:20:48 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 -* [Sun Jun 15 15:20:51 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 -* [Sun Jun 15 15:21:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue May 14 11:06:19 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores +* [Tue May 14 11:06:22 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue May 14 11:07:02 2024] 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 -* [Sun Jun 15 15:21:33 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* [Sun Jun 15 15:21:33 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 -* [Sun Jun 15 15:21:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue May 14 11:07:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue May 14 11:07:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue May 14 11:07:04 2024] 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 -* [Sun Jun 15 15:22:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:07:30 2024] 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 -* [Sun Jun 15 15:22:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue May 14 11:07:36 2024] 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 -* [Sun Jun 15 15:22:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:07:37 2024] 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 -* [Sun Jun 15 15:22:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue May 14 11:07:38 2024] 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 -* [Sun Jun 15 15:22:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue May 14 11:07:39 2024] 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 -* [Sun Jun 15 15:22:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue May 14 11:07:40 2024] 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 @@ -12762,33 +12798,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Sun Jun 15 15:22:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue May 14 11:07:40 2024] 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 -* [Sun Jun 15 15:22:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:08:04 2024] 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 -* [Sun Jun 15 15:22:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue May 14 11:08:10 2024] 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 -* [Sun Jun 15 15:22:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:08:11 2024] 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 -* [Sun Jun 15 15:22:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue May 14 11:08:12 2024] 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 -* [Sun Jun 15 15:22:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue May 14 11:08:13 2024] 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 -* [Sun Jun 15 15:22:45 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* [Sun Jun 15 15:22:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed +* [Tue May 14 11:08:14 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Tue May 14 11:08:14 2024] 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 -* [Sun Jun 15 15:22:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep +* [Tue May 14 11:08:14 2024] 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 -* [Sun Jun 15 15:22:47 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds +* [Tue May 14 11:08:16 2024] 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.* @@ -12900,7 +12936,7 @@ // 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 -* [Sun Jun 15 15:22:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue May 14 11:08:23 2024] 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. @@ -12924,10 +12960,10 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Sun Jun 15 15:22:56 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 -* [Sun Jun 15 15:22:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue May 14 11:08:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue May 14 11:08:25 2024] 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 @@ -12953,80 +12989,80 @@ -skipping training candidate: cdi_i1.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_i1.p1, not unique enough --skipping training candidate: Klp10A_i6.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_i2.p1, not unique enough --skipping training candidate: CG6424_i3.p1, not unique enough +-skipping training candidate: Klp10A_i5.p1, not unique enough +-skipping training candidate: Klp10A_i3.p1, not unique enough +-skipping training candidate: Klp10A_i6.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_i4.p1, not unique enough +-skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough --skipping training candidate: CG33970_i1.p1, not unique enough +-skipping training candidate: CG33970_i2.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough -skipping training candidate: CG12581_i2.p1, not unique enough -skipping training candidate: CG6091_i3.p1, not unique enough --skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: hrg_i3.p1, not unique enough -skipping training candidate: hrg_i2.p1, not unique enough +-skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough --skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough +-skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough -skipping training candidate: l(3)05822_i3.p1, not unique enough --skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i4.p1, not unique enough +-skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough -skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.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: Aldh-III_i1.p1, not unique enough --skipping training candidate: Hsc70-1_i2.p1, not unique enough +-skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough +-skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Est-6_i2.p1, not unique enough -skipping training candidate: S-Lap3_i3.p1, not unique enough -skipping training candidate: S-Lap3_i1.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough -skipping training candidate: CG30438_i1.p1, not unique enough --skipping training candidate: CG30438_i3.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 -skipping training candidate: CG33970_i3.p1, not unique enough -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough --skipping training candidate: Eno_i4.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: CG6091_i2.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_i3.p1, not unique enough +-skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough --skipping training candidate: Galk_i4.p1, not unique enough +-skipping training candidate: Aldh-III_i8.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough +-skipping training candidate: 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_i3.p2, not unique enough +-skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough --skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: CG6424_i3.p2, not unique enough --skipping training candidate: CG6424_i1.p2, not unique enough -skipping training candidate: CG6424_i4.p2, not unique enough +-skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: CG6424_i3.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough @@ -13034,89 +13070,89 @@ -skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i2.p1, not unique enough --skipping training candidate: AdipoR_i5.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: AdipoR_i3.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_i7.p1, not unique enough --skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough +-skipping training candidate: nmo_i6.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_i3.p1, not unique enough --skipping training candidate: CG7564_i1.p1, not unique enough +-skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG7564_i4.p1, not unique enough +-skipping training candidate: CG7564_i1.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough --skipping training candidate: nmo_i2.p1, not unique enough --skipping training candidate: nmo_i5.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: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough --skipping training candidate: CG6024_i1.p1, not unique enough +-skipping training candidate: CG6024_i2.p1, not unique enough -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough -skipping training candidate: ogre_i1.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_i4.p1, not unique enough +-skipping training candidate: ogre_i3.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough --skipping training candidate: Gale_i2.p1, not unique enough +-skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough --skipping training candidate: CG13284_i5.p1, not unique enough +-skipping training candidate: CG13284_i3.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough -skipping training candidate: CG13284_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_i1.p2, not unique enough --skipping training candidate: Klp10A_i6.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_i2.p2, not unique enough +-skipping training candidate: Klp10A_i5.p2, not unique enough +-skipping training candidate: Klp10A_i3.p2, not unique enough +-skipping training candidate: Klp10A_i6.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_i4.p1, not unique enough --skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough +-skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough --skipping training candidate: l(3)05822_i2.p2, not unique enough +-skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: l(3)05822_i3.p2, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough +-skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i6.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_i2.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.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_i2.p2, not unique enough +-skipping training candidate: eIF5B_i1.p2, not unique enough +-skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: Dgk_i6.p2, not unique enough --skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough +-skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: l(1)G0193_i2.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough @@ -13124,25 +13160,25 @@ -skipping training candidate: Dat_i1.p1, not unique enough -skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough --skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough --skipping training candidate: l(3)05822_i2.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: l(3)05822_i4.p3, not unique enough -skipping training candidate: l(3)05822_i3.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough --skipping training candidate: CG6024_i1.p2, not unique enough +-skipping training candidate: CG6024_i2.p2, not unique enough -skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG13887_i2.p1, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG14995_i7.p2, not unique enough -skipping training candidate: Dgk_i5.p3, 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_i5.p2, not unique enough --skipping training candidate: nmo_i6.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: nmo_i3.p2, not unique enough +-skipping training candidate: nmo_i6.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 @@ -13154,471 +13190,472 @@ -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough -skipping training candidate: RpL15_i5.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: RpL15_i2.p1, not unique enough +-skipping training candidate: RpL15_i3.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: Npl4_i1.p3, not unique enough -skipping training candidate: Npl4_i2.p3, not unique enough --skipping training candidate: trc_i2.p2, not unique enough +-skipping training candidate: 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_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough --skipping training candidate: CG14995_i1.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough -skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: CG10237_i2.p2, not unique enough +-skipping training candidate: CG10237_i1.p2, not unique enough -skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: CG10237_i5.p2, not unique enough +-skipping training candidate: Eno_i3.p3, not unique enough +-skipping training candidate: Eno_i5.p3, not unique enough -skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Eno_i6.p3, not unique enough --skipping training candidate: Eno_i2.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: Sec16_i4.p3, not unique enough --skipping training candidate: Sec16_i3.p2, not unique enough +-skipping training candidate: Sec16_i1.p3, not unique enough -skipping training candidate: 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_i1.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough +-skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG30438_i1.p2, not unique enough --skipping training candidate: CG30438_i3.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: 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_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i1.p1, not unique enough --skipping training candidate: ADD1_i2.p2, not unique enough +-skipping training candidate: ADD1_i3.p2, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: Sec16_i3.p3, not unique enough --skipping training candidate: bic_i1.p1, not unique enough +-skipping training candidate: Sec16_i1.p4, not unique enough +-skipping training candidate: bic_i2.p1, not unique enough -skipping training candidate: CG12581_i2.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i4.p1, not unique enough --skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: ctp_i2.p1, not unique enough --skipping training candidate: hrg_i4.p2, not unique enough +-skipping training candidate: ctp_i3.p1, not unique enough +-skipping training candidate: ctp_i4.p1, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough +-skipping training candidate: hrg_i4.p2, not unique enough +-skipping training candidate: Eno_i3.p4, not unique enough +-skipping training candidate: Eno_i5.p4, not unique enough -skipping training candidate: Eno_i4.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Eno_i2.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: Klp10A_i1.p3, not unique enough --skipping training candidate: Klp10A_i6.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_i2.p4, not unique enough --skipping training candidate: Calx_i8.p2, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough +-skipping training candidate: Klp10A_i5.p3, not unique enough +-skipping training candidate: Klp10A_i3.p3, not unique enough +-skipping training candidate: Klp10A_i6.p3, not unique enough +-skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Calx_i2.p2, not unique enough --skipping training candidate: Calx_i5.p2, not unique enough +-skipping training candidate: Calx_i6.p2, not unique enough -skipping training candidate: Calx_i3.p2, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough +-skipping training candidate: Calx_i5.p2, not unique enough +-skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough -skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough --skipping training candidate: CG7564_i3.p3, 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.p5, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough --skipping training candidate: Gale_i2.p2, not unique enough --skipping training candidate: eIF5B_i5.p3, not unique enough --skipping training candidate: eIF5B_i1.p3, not unique enough +-skipping training candidate: CG7564_i1.p2, not unique enough +-skipping training candidate: CG7564_i1.p3, not unique enough +-skipping training candidate: Gale_i1.p2, not unique enough -skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i1.p3, not unique enough +-skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough --skipping training candidate: AdipoR_i4.p2, not unique enough --skipping training candidate: CG6424_i3.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: AdipoR_i3.p2, not unique enough -skipping training candidate: CG6424_i4.p3, not unique enough --skipping training candidate: Tm1_i13.p2, not unique enough --skipping training candidate: Tm1_i14.p2, not unique enough +-skipping training candidate: CG6424_i2.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: Tm1_i16.p2, not unique enough --skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Tm1_i5.p2, not unique enough +-skipping training candidate: Tm1_i14.p2, not unique enough -skipping training candidate: Dgk_i2.p5, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i7.p5, not unique enough +-skipping training candidate: Dgk_i1.p4, not unique enough -skipping training candidate: cdi_i2.p3, not unique enough --skipping training candidate: eff_i2.p1, not unique enough +-skipping training candidate: eff_i3.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_i5.p4, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i4.p5, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough --skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: eIF5B_i1.p4, not unique enough +-skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough -skipping training candidate: Sec16_i5.p4, not unique enough --skipping training candidate: Sec16_i3.p4, not unique enough --skipping training candidate: CG32082_i4.p2, not unique enough --skipping training candidate: CG32082_i3.p2, not unique enough -skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough +-skipping training candidate: CG32082_i4.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough --skipping training candidate: CG3530_i1.p2, not unique enough --skipping training candidate: Dgk_i2.p6, not unique enough --skipping training candidate: l(3)05822_i2.p4, not unique enough +-skipping training candidate: CG3530_i2.p2, not unique enough +-skipping training candidate: Dgk_i7.p6, not unique enough +-skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: sqd_i1.p2, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough --skipping training candidate: CG7564_i1.p4, not unique enough +-skipping training candidate: CG7564_i2.p6, not unique enough -skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough -skipping training candidate: cdi_i2.p4, not unique enough --skipping training candidate: CG6091_i1.p2, not unique enough +-skipping training candidate: CG6091_i4.p2, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough -skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i2.p2, not unique enough -skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough --skipping training candidate: Cnx99A_i4.p2, not unique enough +-skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough --skipping training candidate: Sec16_i3.p5, not unique enough --skipping training candidate: ogre_i6.p2, not unique enough --skipping training candidate: CG6024_i1.p3, not unique enough --skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: ogre_i3.p2, not unique enough +-skipping training candidate: CG6024_i2.p3, not unique enough -skipping training candidate: hrg_i3.p3, not unique enough +-skipping training candidate: hrg_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i3.p2, not unique enough --skipping training candidate: CG6091_i1.p3, not unique enough +-skipping training candidate: CG6091_i4.p3, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough --skipping training candidate: CG33970_i1.p2, not unique enough +-skipping training candidate: CG33970_i2.p2, not unique enough -skipping training candidate: CG33970_i3.p2, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: Aldh-III_i8.p2, not unique enough -skipping training candidate: Aldh-III_i11.p2, not unique enough --skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i1.p2, not unique enough +-skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough +-skipping training candidate: CG13284_i1.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_i1.p2, not unique enough +-skipping training candidate: Lip4_i3.p2, not unique enough -skipping training candidate: Lip4_i2.p2, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough --skipping training candidate: Dgk_i6.p5, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough --skipping training candidate: Tm1_i13.p3, not unique enough --skipping training candidate: Tm1_i14.p3, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Tm1_i16.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: Tm1_i5.p3, not unique enough +-skipping training candidate: Tm1_i14.p3, not unique enough +-skipping training candidate: CG8312_i2.p3, not unique enough +-skipping training candidate: CG8312_i2.p4, not unique enough -skipping training candidate: CG8312_i4.p3, not unique enough -skipping training candidate: CG8312_i4.p4, not unique enough --skipping training candidate: Klp10A_i1.p4, not unique enough --skipping training candidate: Klp10A_i6.p4, not unique enough --skipping training candidate: Klp10A_i5.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: Klp10A_i4.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough --skipping training candidate: eff_i2.p2, not unique enough +-skipping training candidate: Klp10A_i5.p4, not unique enough +-skipping training candidate: Klp10A_i3.p4, not unique enough +-skipping training candidate: Klp10A_i6.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_i1.p2, not unique enough --skipping training candidate: CG14995_i4.p4, not unique enough --skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough +-skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG14995_i5.p5, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough --skipping training candidate: CG6424_i3.p5, not unique enough --skipping training candidate: CG6424_i1.p5, not unique enough +-skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG6424_i4.p4, not unique enough +-skipping training candidate: CG6424_i2.p4, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough -skipping training candidate: CG12581_i2.p3, not unique enough --skipping training candidate: CG32082_i4.p5, not unique enough --skipping training candidate: CG32082_i3.p3, not unique enough -skipping training candidate: CG32082_i1.p3, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough +-skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: Cnx99A_i3.p3, not unique enough -skipping training candidate: Cnx99A_i1.p3, not unique enough +-skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Cdep_i4.p2, not unique enough --skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough --skipping training candidate: CG33970_i1.p3, not unique enough +-skipping training candidate: CG33970_i2.p3, not unique enough -skipping training candidate: CG33970_i3.p3, not unique enough --skipping training candidate: Sec16_i1.p7, not unique enough +-skipping training candidate: Sec16_i3.p6, 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_i1.p7, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough -skipping training candidate: Sec16_i5.p6, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough --skipping training candidate: CG6024_i1.p4, not unique enough --skipping training candidate: Myo61F_i1.p2, not unique enough --skipping training candidate: Myo61F_i3.p2, not unique enough +-skipping training candidate: CG6024_i2.p4, not unique enough -skipping training candidate: Myo61F_i2.p2, not unique enough +-skipping training candidate: Myo61F_i4.p2, not unique enough +-skipping training candidate: Myo61F_i1.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough -skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: Cnx99A_i1.p4, not unique enough --skipping training candidate: CG13887_i4.p2, not unique enough +-skipping training candidate: CG13887_i2.p2, not unique enough -skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough -skipping training candidate: CG6145_i4.p2, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough -skipping training candidate: CG6145_i1.p2, not unique enough --skipping training candidate: Calx_i8.p3, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: Calx_i2.p3, not unique enough --skipping training candidate: Calx_i5.p3, not unique enough +-skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: Calx_i3.p3, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough +-skipping training candidate: Calx_i5.p3, not unique enough +-skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: Calx_i9.p3, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough -skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: mge_i2.p2, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough --skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i4.p3, not unique enough --skipping training candidate: Aldh-III_i2.p2, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough +-skipping training candidate: AdipoR_i3.p3, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough --skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough -skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i10.p3, not unique enough --skipping training candidate: Cdep_i4.p3, not unique enough --skipping training candidate: Cdep_i3.p4, 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: Cdep_i2.p9, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough +-skipping training candidate: Cdep_i4.p3, not unique enough -skipping training candidate: hrg_i3.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough +-skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i2.p4, not unique enough --skipping training candidate: Sec16_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: Sec16_i4.p8, not unique enough -skipping training candidate: Sec16_i4.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_i2.p8, not unique enough -skipping training candidate: Sec16_i2.p9, not unique enough -skipping training candidate: Sec16_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough --skipping training candidate: Sec16_i3.p7, not unique enough --skipping training candidate: Sec16_i3.p8, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough --skipping training candidate: CG6091_i1.p4, not unique enough +-skipping training candidate: CG6091_i4.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough -skipping training candidate: CG6091_i3.p4, not unique enough -skipping training candidate: CanB2_i1.p2, not unique enough --skipping training candidate: IP3K1_i2.p2, not unique enough --skipping training candidate: Klp10A_i1.p6, not unique enough --skipping training candidate: Klp10A_i6.p5, not unique enough --skipping training candidate: Klp10A_i5.p5, not unique enough +-skipping training candidate: IP3K1_i1.p3, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough --skipping training candidate: Klp10A_i2.p8, not unique enough +-skipping training candidate: Klp10A_i5.p5, not unique enough +-skipping training candidate: Klp10A_i3.p5, not unique enough +-skipping training candidate: Klp10A_i6.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_i4.p4, not unique enough --skipping training candidate: Cdep_i3.p5, not unique enough +-skipping training candidate: Cdep_i2.p10, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough +-skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Est-6_i2.p2, not unique enough --skipping training candidate: Klp10A_i1.p7, not unique enough --skipping training candidate: Klp10A_i6.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_i2.p9, not unique enough +-skipping training candidate: Klp10A_i5.p6, not unique enough +-skipping training candidate: Klp10A_i3.p6, not unique enough +-skipping training candidate: Klp10A_i6.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_i2.p3, not unique enough +-skipping training candidate: ADD1_i3.p4, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough --skipping training candidate: Cnx99A_i4.p3, not unique enough --skipping training candidate: Myo61F_i1.p3, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough --skipping training candidate: Myo61F_i1.p4, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough +-skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Myo61F_i1.p3, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough --skipping training candidate: bic_i1.p3, not unique enough +-skipping training candidate: Myo61F_i4.p4, not unique enough +-skipping training candidate: Myo61F_i1.p4, not unique enough +-skipping training candidate: bic_i2.p2, not unique enough -skipping training candidate: CG10082_i1.p5, not unique enough --skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: CG32082_i3.p4, not unique enough -skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough +-skipping training candidate: CG32082_i4.p6, 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_i4.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_i5.p6, not unique enough -skipping training candidate: Eno_i1.p6, not unique enough --skipping training candidate: Sec16_i1.p10, not unique enough --skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough --skipping training candidate: Dgk_i6.p6, not unique enough +-skipping training candidate: Sec16_i4.p10, not unique enough +-skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i3.p6, 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: CG33970_i1.p4, 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_i3.p6, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Dgk_i1.p6, 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: Dgk_i3.p7, not unique enough --skipping training candidate: His4r_i1.p1, not unique enough +-skipping training candidate: Dgk_i1.p7, not unique enough +-skipping training candidate: His4r_i2.p1, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: His4r_i3.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_i4.p6, not unique enough -skipping training candidate: hrg_i3.p5, not unique enough +-skipping training candidate: hrg_i4.p6, not unique enough +-skipping training candidate: CG8136_i4.p2, not unique enough -skipping training candidate: CG8136_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_i1.p5, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough --skipping training candidate: CG6091_i1.p5, not unique enough +-skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: Myo61F_i1.p5, not unique enough +-skipping training candidate: CG6091_i4.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough -skipping training candidate: CG6091_i3.p5, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough -skipping training candidate: CG6145_i4.p3, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i1.p3, not unique enough --skipping training candidate: gukh_i1.p4, not unique enough --skipping training candidate: sqd_i5.p4, not unique enough +-skipping training candidate: gukh_i2.p3, not unique enough +-skipping training candidate: sqd_i3.p3, not unique enough -skipping training candidate: CG33125_i1.p4, not unique enough --skipping training candidate: gukh_i1.p5, not unique enough +-skipping training candidate: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Sun Jun 15 15:22:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue May 14 11:08:26 2024] 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 -* [Sun Jun 15 15:22:57 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 -* [Sun Jun 15 15:22:57 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 -* [Sun Jun 15 15:23:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue May 14 11:08:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Tue May 14 11:08:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue May 14 11:08:33 2024] 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 -* [Sun Jun 15 15:23:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Sun Jun 15 15:23:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Sun Jun 15 15:23:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue May 14 11:08:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue May 14 11:08:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue May 14 11:08:34 2024] 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 -* [Sun Jun 15 15:23:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:08:58 2024] 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 -* [Sun Jun 15 15:23:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue May 14 11:09:05 2024] 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 -* [Sun Jun 15 15:23:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue May 14 11:09:06 2024] 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 -* [Sun Jun 15 15:23:38 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 || : +* [Tue May 14 11:09:07 2024] 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 -* [Sun Jun 15 15:23:38 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 || : +* [Tue May 14 11:09:07 2024] 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 -* [Sun Jun 15 15:23:39 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 +* [Tue May 14 11:09:08 2024] 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: -1.04054537194645 instead of -3.42546936606421 --feature swap of score: -1.54991160622372 instead of -3.27835248355382 --feature swap of score: -1.85758452719583 instead of -2.7598070054252 --feature swap of score: -1.41248090491035 instead of -1.7197582976389 --feature swap of score: -0.730916824770562 instead of -1.44757767806614 --feature swap of score: -0.881695866661337 instead of -1.29905863067992 --feature swap of score: 2.07528344859266 instead of -1.15603258564484 --feature swap of score: -0.479124302890981 instead of -1.14629188661356 --feature swap of score: 2.79832429443716 instead of -0.995667189061782 --feature swap of score: -0.568940086555578 instead of -2.43571049061737 --feature swap of score: 2.48600957439542 instead of -1.17628923826732 --feature swap of score: -1.10785244441238 instead of -1.29731922798982 --feature swap of score: -0.862852992207894 instead of -1.50793087784975 --feature swap of score: 0.102713186286192 instead of -1.13437583507827 --feature swap of score: 1.60618790625671 instead of -0.970542330034068 --feature swap of score: 2.02969894266909 instead of -1.17490697067849 --feature swap of score: -1.05541380264798 instead of -1.24879510621116 --feature swap of score: -0.049495538116431 instead of -1.20478444006614 --feature swap of score: -0.661819318353942 instead of -1.38558851024455 --feature swap of score: -0.0497500176259531 instead of -0.940041162048007 --feature swap of score: 0.0182758175595917 instead of -0.853070304515272 --feature swap of score: 0.613265182733336 instead of -0.663362675528937 --feature swap of score: 3.50457220522255 instead of -0.45763757306792 --feature swap of score: 1.00827573919896 instead of -0.850527020351268 --feature swap of score: -0.608071204210007 instead of -0.894673126935403 --feature swap of score: 2.5477895261183 instead of -0.720564406290823 --feature swap of score: 0.127012506724005 instead of -0.743631737803706 --feature swap of score: 0.074102691294917 instead of 0.0579407511950992 --feature swap of score: 1.66397712634915 instead of -0.0655925495909893 --feature swap of score: 1.35995991016169 instead of 0.027662564191888 --feature swap of score: 0.221382539272919 instead of -0.129398014304041 --feature swap of score: 3.6909305861938 instead of 0.0185926377633254 --feature swap of score: 0.0767324241816106 instead of -0.156905881179781 --feature swap of score: 1.12744554705998 instead of -0.234075409760546 --feature swap of score: 0.832304583287398 instead of -0.417192889389524 --feature swap of score: 0.779571954693575 instead of -0.545711881524266 --feature swap of score: 0.497231709750662 instead of -0.877037602707237 --feature swap of score: -0.0907756630978618 instead of -0.809864456707278 --feature swap of score: -0.4722188622154 instead of -0.908090835259826 --feature swap of score: 0.320678158523425 instead of -0.721371130514422 --feature swap of score: 1.28313733531235 instead of -1.40234756828138 --feature swap of score: 2.02666202946951 instead of -0.436096989507964 --feature swap of score: 0.0900169094008027 instead of -0.25070246241415 --feature swap of score: 2.04964335073739 instead of -0.0193286760348477 --feature swap of score: -0.206314852430428 instead of -0.234255180029227 --feature swap of score: 0.311040130301499 instead of -0.249872745956267 --feature swap of score: -0.289570657896949 instead of -0.296844079928233 --feature swap of score: -0.080491263531765 instead of -0.341064778496223 --feature swap of score: 1.80891940759287 instead of 0.2917752175465 --feature swap of score: 0.690214906050519 instead of -0.172664746099929 --feature swap of score: 0.463056144664725 instead of 0.294521502604554 --feature swap of score: 4.04626420413603 instead of 0.550706689365746 --feature swap of score: 0.863194232039065 instead of 0.43005814007317 --feature swap of score: 2.16889877528902 instead of 0.409798805750465 --feature swap of score: 1.04914388795095 instead of 0.862879569558732 --feature swap of score: 1.34239799755414 instead of 0.681596044665194 --feature swap of score: 6.94681566314834 instead of 0.607585788720217 --feature swap of score: 1.30258356820905 instead of 0.502226391722617 --feature swap of score: 8.10498406811397 instead of 0.566745986990527 --feature swap of score: 2.78204651297375 instead of 0.326520599299134 --num feature swaps: 60 -* [Sun Jun 15 15:23:39 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/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: -1.53839921762058 instead of -3.41347771265998 +-feature swap of score: -1.36266372730403 instead of -3.49710514888405 +-feature swap of score: -1.87887009978679 instead of -3.03438121347773 +-feature swap of score: -1.57487831462515 instead of -1.62863597843695 +-feature swap of score: -0.968464452047464 instead of -1.26335058378188 +-feature swap of score: -0.744278885986601 instead of -1.31115058822073 +-feature swap of score: 1.9001322045274 instead of -1.04096081669527 +-feature swap of score: -0.659879108857394 instead of -0.975226895284329 +-feature swap of score: 2.78824337494789 instead of -0.982456817361862 +-feature swap of score: -0.907570851285577 instead of -2.43618336954772 +-feature swap of score: 2.0843560736805 instead of -1.10598557770733 +-feature swap of score: -0.672220008565839 instead of -1.14022952693813 +-feature swap of score: 0.264235341549048 instead of -1.31558766309999 +-feature swap of score: 1.02704016063408 instead of -0.986284115358614 +-feature swap of score: 1.7855897730058 instead of -1.06808776532389 +-feature swap of score: 0.268721003507684 instead of -1.10357021762414 +-feature swap of score: -0.117560443408581 instead of -1.31466448108972 +-feature swap of score: 0.244270455452909 instead of -1.26428473766038 +-feature swap of score: 0.135935258929865 instead of -0.633422308538949 +-feature swap of score: 0.294416397489477 instead of -0.490231417447247 +-feature swap of score: 3.36171144643621 instead of -0.371395893847987 +-feature swap of score: 1.92516600366448 instead of -0.444364284991692 +-feature swap of score: 0.760662071285355 instead of -0.36516306615515 +-feature swap of score: 2.61451096627198 instead of -0.368787832363167 +-feature swap of score: -0.380152527283564 instead of -0.822051695757556 +-feature swap of score: 0.636458574970516 instead of -0.224434139245553 +-feature swap of score: 2.43186881322233 instead of -0.332167533835865 +-feature swap of score: 1.18494131623276 instead of -0.225954015815342 +-feature swap of score: 1.27183261908235 instead of -0.491873703965225 +-feature swap of score: 0.382043011924024 instead of -0.490873748674976 +-feature swap of score: 3.10412101988533 instead of -0.375771314042884 +-feature swap of score: 0.307824757342104 instead of -0.666604607470626 +-feature swap of score: 0.8635124256731 instead of -0.833956438076007 +-feature swap of score: -0.974461413010491 instead of -1.01160341182304 +-feature swap of score: 1.20703329850789 instead of -0.861761586776321 +-feature swap of score: 1.0605070349294 instead of -0.822844505280546 +-feature swap of score: 0.58290010225644 instead of -0.513508797259434 +-feature swap of score: 0.159509189807005 instead of -0.733657150395251 +-feature swap of score: 0.997645802320798 instead of -0.434266001719911 +-feature swap of score: -0.0348198566587578 instead of -0.436308577093216 +-feature swap of score: 2.3262071970915 instead of -0.322131547287056 +-feature swap of score: 0.947502953973523 instead of 0.00136945432374463 +-feature swap of score: 1.4756112263548 instead of 0.101140750106468 +-feature swap of score: 0.392348574079235 instead of 0.280435365243569 +-feature swap of score: 1.00060528612217 instead of 0.267938730428501 +-feature swap of score: 0.859267437464636 instead of 0.122780787697128 +-feature swap of score: 1.59397168307414 instead of 0.143648263530568 +-feature swap of score: 1.65106241125188 instead of 0.414684331549145 +-feature swap of score: 0.364171668977475 instead of 0.198049641099879 +-feature swap of score: 2.92544128356287 instead of 0.48549176433224 +-feature swap of score: 0.706242358698801 instead of 0.296830944141105 +-feature swap of score: 2.12176077668468 instead of 0.51802149715925 +-feature swap of score: 2.0496964470909 instead of 0.491750211223961 +-feature swap of score: 1.62523514692843 instead of 0.631074250571693 +-feature swap of score: 0.816456123659278 instead of 0.744717868806891 +-feature swap of score: 1.42398317688146 instead of 0.594474846451706 +-feature swap of score: 7.42365830160766 instead of 0.74834784187376 +-feature swap of score: 1.43137445488265 instead of 0.476221877402247 +-feature swap of score: 0.544219084581322 instead of 0.35984612572351 +-feature swap of score: 8.86330482813459 instead of 0.321898291515912 +-feature swap of score: 1.58298408471993 instead of 0.697071130044489 +-num feature swaps: 61 +* [Tue May 14 11:09:08 2024] 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 -* [Sun Jun 15 15:24:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:09:31 2024] 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 -* [Sun Jun 15 15:24:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue May 14 11:09:37 2024] 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 -* [Sun Jun 15 15:24:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue May 14 11:09:38 2024] 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 -* [Sun Jun 15 15:24:11 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 || : +* [Tue May 14 11:09:39 2024] 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 -* [Sun Jun 15 15:24:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue May 14 11:09:40 2024] 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: 13 -* [Sun Jun 15 15:24:12 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* [Sun Jun 15 15:24:12 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: 12 +* [Tue May 14 11:09:40 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Tue May 14 11:09:40 2024] 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 -* [Sun Jun 15 15:24:12 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 +* [Tue May 14 11:09:40 2024] 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 -* [Sun Jun 15 15:24:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds +* [Tue May 14 11:09:41 2024] 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.* @@ -13767,8 +13804,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-deb: building package 'transdecoder' in '../transdecoder_5.7.1-2_all.deb'. +dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../transdecoder_5.7.1-2_arm64.buildinfo dpkg-genchanges --build=binary -O../transdecoder_5.7.1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13776,12 +13813,14 @@ 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/3914991/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3914991/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/1546464 and its subdirectories -I: Current time: Sun Jun 15 15:24:35 -12 2025 -I: pbuilder-time-stamp: 1750044275 +I: removing directory /srv/workspace/pbuilder/3914991 and its subdirectories +I: Current time: Tue May 14 11:10:01 +14 2024 +I: pbuilder-time-stamp: 1715634601