Diff of the two buildlogs: -- --- b1/build.log 2024-05-26 10:06:27.531655971 +0000 +++ b2/build.log 2024-05-26 10:17:46.490768621 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 25 21:47:15 -12 2024 -I: pbuilder-time-stamp: 1716716835 +I: Current time: Sun Jun 29 06:29:30 +14 2025 +I: pbuilder-time-stamp: 1751128170 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/1555680/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1081689/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 28 16:29 /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/1081689/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1081689/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='80439b8c522542d4831bd8a41689bfa1' - 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='1555680' - PS1='# ' - PS2='> ' + INVOCATION_ID=61850359234a43ab81730b5e5ea4961f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1081689 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.z0c8eVSb/pbuilderrc_dbAN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z0c8eVSb/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.z0c8eVSb/pbuilderrc_v5lO --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z0c8eVSb/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1555680/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 28 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1081689/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -288,7 +320,7 @@ Get: 164 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 132 MB in 3s (39.6 MB/s) +Fetched 132 MB in 13s (10.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19718 files and directories currently installed.) @@ -840,8 +872,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun May 26 09:49:06 UTC 2024. -Universal Time is now: Sun May 26 09:49:06 UTC 2024. +Local time is now: Sat Jun 28 16:31:21 UTC 2025. +Universal Time is now: Sat Jun 28 16:31:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -1000,7 +1032,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes +I: user script /srv/workspace/pbuilder/1081689/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1081689/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes dpkg-buildpackage: info: source package transdecoder dpkg-buildpackage: info: source version 5.7.1-2 dpkg-buildpackage: info: source distribution unstable @@ -1022,7 +1058,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j20 test + make -j42 test make[2]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' @@ -1064,7 +1100,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Sat May 25 21:49:32 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 +* [Sun Jun 29 06:31:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -1116,13 +1152,13 @@ fi -Building a new DB, current time: 05/25/2024 21:49:33 +Building a new DB, current time: 06/29/2025 06:31:37 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 0.016552 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00954819 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1197,8 +1233,8 @@ 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: 863.46 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1282.56 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1255,8 +1291,8 @@ 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: 817.47 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1361.40 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1320,8 +1356,8 @@ 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: 1347.23 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1854.64 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1382,7 +1418,7 @@ 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: 1280.91 +# Mc/sec: 1699.00 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1443,7 +1479,7 @@ 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: 418.79 +# Mc/sec: 538.31 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1493,8 +1529,8 @@ 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: 341.97 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 534.79 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1558,8 +1594,8 @@ 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: 1456.25 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1387.01 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1611,8 +1647,8 @@ 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: 383.85 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 684.41 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1663,7 +1699,7 @@ 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: 1213.56 +# Mc/sec: 1481.63 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1719,8 +1755,8 @@ 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: 1301.82 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1736.77 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1808,8 +1844,8 @@ 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: 871.33 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1453.94 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1893,8 +1929,8 @@ 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: 966.34 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1608.67 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1950,8 +1986,8 @@ 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: 588.52 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 835.82 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -2007,8 +2043,8 @@ 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: 00:00:00.02 -# Mc/sec: 571.74 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 711.63 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2065,7 +2101,7 @@ 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: 1460.20 +# Mc/sec: 2705.60 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2109,8 +2145,8 @@ 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: 1407.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2209.50 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2163,7 +2199,7 @@ 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: 1668.45 +# Mc/sec: 2600.97 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2207,8 +2243,8 @@ 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: 1114.50 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2163.73 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2269,7 +2305,7 @@ 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: 994.98 +# Mc/sec: 1572.97 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2320,7 +2356,7 @@ 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: 786.00 +# Mc/sec: 1097.36 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2432,8 +2468,8 @@ 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: 606.57 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1216.55 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2479,8 +2515,8 @@ 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: 1428.89 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2106.18 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2546,8 +2582,8 @@ 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: 1133.02 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1558.91 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2586,7 +2622,7 @@ 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: 2364.08 +# Mc/sec: 2731.79 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2662,8 +2698,8 @@ 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: 835.58 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1235.88 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2715,8 +2751,8 @@ 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: 1476.35 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2031.58 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2800,8 +2836,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 303.16 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 574.79 // Query: DLH [M=217] Accession: PF01738.17 @@ -2848,8 +2884,8 @@ 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: 1836.47 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2969.95 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2896,7 +2932,7 @@ 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: 1280.25 +# Mc/sec: 1797.24 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2946,7 +2982,7 @@ 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: 1787.38 +# Mc/sec: 2744.03 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2989,7 +3025,7 @@ 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: 1814.56 +# Mc/sec: 2999.10 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3035,7 +3071,7 @@ 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: 768.59 +# Mc/sec: 1195.23 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3073,7 +3109,7 @@ 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: 1983.36 +# Mc/sec: 2665.76 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3125,7 +3161,7 @@ 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: 1036.23 +# Mc/sec: 1191.70 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3163,7 +3199,7 @@ 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: 1100.33 +# Mc/sec: 1557.27 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3201,7 +3237,7 @@ 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: 1735.02 +# Mc/sec: 2243.78 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3252,7 +3288,7 @@ 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: 1517.67 +# Mc/sec: 1646.48 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3289,8 +3325,8 @@ 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: 2738.45 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3087.91 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3351,7 +3387,7 @@ 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: 1463.56 +# Mc/sec: 2502.27 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3396,7 +3432,7 @@ 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: 1255.38 +# Mc/sec: 2549.05 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3452,8 +3488,8 @@ 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: 1309.55 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2494.88 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3507,8 +3543,8 @@ 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: 530.15 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1004.49 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3545,8 +3581,8 @@ 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: 2200.12 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3476.32 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3623,7 +3659,7 @@ 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: 1562.30 +# Mc/sec: 2257.34 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3687,8 +3723,8 @@ 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: 435.77 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 572.20 // Query: FPP [M=866] Accession: PF05911.10 @@ -3738,8 +3774,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 1062.79 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2243.94 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3792,7 +3828,7 @@ 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: 1452.41 +# Mc/sec: 1767.57 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3915,8 +3951,8 @@ 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 409.83 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 730.78 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3955,7 +3991,7 @@ 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: 965.45 +# Mc/sec: 1238.24 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4045,8 +4081,8 @@ 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: 00:00:00.03 -# Mc/sec: 432.61 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 818.14 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4096,8 +4132,8 @@ 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: 356.06 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 628.03 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4158,7 +4194,7 @@ 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: 934.00 +# Mc/sec: 1479.20 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4263,7 +4299,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 492.98 +# Mc/sec: 889.20 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4310,8 +4346,8 @@ 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: 1325.87 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2323.98 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4385,8 +4421,8 @@ 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: 832.44 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1404.29 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4457,7 +4493,7 @@ 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: 1212.01 +# Mc/sec: 1924.21 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4504,8 +4540,8 @@ 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: 586.39 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1099.89 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4575,8 +4611,8 @@ 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: 211.53 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 384.52 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4627,7 +4663,7 @@ 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: 1965.07 +# Mc/sec: 2816.21 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4677,8 +4713,8 @@ 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: 2132.56 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3098.40 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4716,8 +4752,8 @@ 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: 1466.48 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2055.32 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4762,7 +4798,7 @@ 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: 1327.84 +# Mc/sec: 2059.52 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4814,7 +4850,7 @@ 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: 1003.09 +# Mc/sec: 1557.94 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4896,8 +4932,8 @@ 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: 616.03 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1235.32 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4997,8 +5033,8 @@ 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 440.24 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 962.38 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5053,7 +5089,7 @@ 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: 1004.76 +# Mc/sec: 1755.71 // Query: IBR [M=62] Accession: PF01485.20 @@ -5091,7 +5127,7 @@ 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: 1213.71 +# Mc/sec: 2207.42 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5138,8 +5174,8 @@ 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: 689.42 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1342.81 // Query: malic [M=182] Accession: PF00390.18 @@ -5177,8 +5213,8 @@ 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: 2583.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 4180.43 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5215,8 +5251,8 @@ 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: 786.00 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1527.97 // Query: MatE [M=161] Accession: PF01554.17 @@ -5301,7 +5337,7 @@ 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: 1025.50 +# Mc/sec: 1634.91 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5338,8 +5374,8 @@ 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: 1961.18 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3393.26 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5513,8 +5549,8 @@ 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 0.01s 00:00:00.08 Elapsed: 00:00:00.08 -# Mc/sec: 133.71 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.04 +# Mc/sec: 268.90 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5556,8 +5592,8 @@ 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: 1288.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2535.53 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5613,8 +5649,8 @@ 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: 775.69 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1395.87 // Query: MIP [M=227] Accession: PF00230.19 @@ -5665,7 +5701,7 @@ 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: 1367.62 +# Mc/sec: 2803.81 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5718,7 +5754,7 @@ 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: 1043.11 +# Mc/sec: 1344.81 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5808,8 +5844,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1366.01 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2545.01 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5847,7 +5883,7 @@ 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: 1233.38 +# Mc/sec: 2343.00 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5884,8 +5920,8 @@ 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: 1952.25 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3645.44 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5938,7 +5974,7 @@ 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: 1711.60 +# Mc/sec: 2978.76 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5976,7 +6012,7 @@ 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: 2451.93 +# Mc/sec: 4303.62 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6096,8 +6132,8 @@ 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 426.42 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1266.10 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6147,8 +6183,8 @@ 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: 532.64 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3085.51 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6218,8 +6254,8 @@ 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: 408.30 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2671.96 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6272,7 +6308,7 @@ 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: 564.10 +# Mc/sec: 1061.16 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6334,8 +6370,8 @@ 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: 00:00:00.01 -# Mc/sec: 900.58 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1719.68 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6437,8 +6473,8 @@ 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: 00:00:00.02 -# Mc/sec: 176.19 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 348.35 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6485,8 +6521,8 @@ 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: 1386.20 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2111.88 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6537,7 +6573,7 @@ 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: 788.27 +# Mc/sec: 1116.04 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6588,7 +6624,7 @@ 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: 1309.69 +# Mc/sec: 1797.63 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6639,7 +6675,7 @@ 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: 1892.49 +# Mc/sec: 2101.35 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6684,7 +6720,7 @@ 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: 1834.28 +# Mc/sec: 3275.73 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6731,7 +6767,7 @@ 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: 777.72 +# Mc/sec: 1600.76 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6795,8 +6831,8 @@ 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: 334.14 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 719.02 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6841,7 +6877,7 @@ 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: 1133.54 +# Mc/sec: 2332.72 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6893,8 +6929,8 @@ 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: 604.85 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1156.88 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6939,7 +6975,7 @@ 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: 1921.93 +# Mc/sec: 2641.30 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7039,8 +7075,8 @@ 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: 00:00:00.04 -# Mc/sec: 304.95 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 613.78 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7084,8 +7120,8 @@ 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: 494.59 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 881.81 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7138,7 +7174,7 @@ 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: 1762.43 +# Mc/sec: 1968.74 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7211,8 +7247,8 @@ 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: 277.94 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 519.95 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7273,7 +7309,7 @@ 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: 1439.50 +# Mc/sec: 2242.42 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7318,7 +7354,7 @@ 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: 1595.72 +# Mc/sec: 2454.98 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7371,7 +7407,7 @@ 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: 1492.90 +# Mc/sec: 2722.86 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7409,7 +7445,7 @@ 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: 3392.42 +# Mc/sec: 6241.19 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7452,7 +7488,7 @@ 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: 2060.19 +# Mc/sec: 3295.23 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7514,8 +7550,8 @@ 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: 00:00:00.03 -# Mc/sec: 472.24 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 664.74 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7552,8 +7588,8 @@ 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: 2121.17 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3394.58 // Query: Usher [M=551] Accession: PF00577.19 @@ -7597,8 +7633,8 @@ 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: 1673.83 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2614.78 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7645,7 +7681,7 @@ 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: 511.21 +# Mc/sec: 706.54 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7690,7 +7726,7 @@ 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: 491.90 +# Mc/sec: 824.85 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -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: 567.73 +# Mc/sec: 1115.85 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7790,7 +7826,7 @@ 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: 583.55 +# Mc/sec: 1087.14 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7828,8 +7864,8 @@ 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: 332.23 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 735.53 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7881,7 +7917,7 @@ 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: 481.08 +# Mc/sec: 1233.60 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7928,8 +7964,8 @@ 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: 921.44 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1501.52 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7968,14 +8004,14 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 906.93 +# Mc/sec: 1360.29 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Sat May 25 21:49:35 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 -* [Sat May 25 21:49:35 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 +* [Sun Jun 29 06:31:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:31:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -8002,39 +8038,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Sat May 25 21:49:35 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 +* [Sun Jun 29 06:31:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 37 -* [Sat May 25 21:49:35 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 -* [Sat May 25 21:49:36 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 -* [Sat May 25 21:49:37 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 +* [Sun Jun 29 06:31:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:31:39 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 29 06:31:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Sat May 25 21:49:37 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* [Sat May 25 21:49:37 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 -* [Sat May 25 21:49:38 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 +* [Sun Jun 29 06:31:40 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 29 06:31:40 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 29 06:31:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:50:15 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 +* [Sun Jun 29 06:32:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat May 25 21:50:23 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 || : +* [Sun Jun 29 06:32:18 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat May 25 21:50:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sun Jun 29 06:32:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat May 25 21:50:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sun Jun 29 06:32:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:50:28 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 || : +* [Sun Jun 29 06:32:22 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 || : Loading required package: grid null device 1 -* [Sat May 25 21:50:29 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 +* [Sun Jun 29 06:32:23 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 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 @@ -8044,33 +8080,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Sat May 25 21:50:29 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 +* [Sun Jun 29 06:32:23 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:51:04 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/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 +* [Sun Jun 29 06:32:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat May 25 21:51:12 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 || : +* [Sun Jun 29 06:32:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat May 25 21:51:14 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 +* [Sun Jun 29 06:32:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat May 25 21:51:16 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 || : +* [Sun Jun 29 06:32:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:51:17 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 +* [Sun Jun 29 06:32:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 1 -* [Sat May 25 21:51:17 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* [Sat May 25 21:51:17 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 +* [Sun Jun 29 06:32:58 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 29 06:32:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Sat May 25 21:51:17 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 +* [Sun Jun 29 06:32:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Sat May 25 21:51:17 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 +* [Sun Jun 29 06:32:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* @@ -8162,7 +8198,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Sat May 25 21:51:18 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 +* [Sun Jun 29 06:32:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -8186,8 +8222,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Sat May 25 21:51:22 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 -* [Sat May 25 21:51:22 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 +* [Sun Jun 29 06:33:01 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 29 06:33:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough @@ -8862,37 +8898,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Sat May 25 21:51:23 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 +* [Sun Jun 29 06:33:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 -* [Sat May 25 21:51:23 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 -* [Sat May 25 21:51:25 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 -* [Sat May 25 21:51:39 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 +* [Sun Jun 29 06:33:02 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 29 06:33:03 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 29 06:33:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat May 25 21:51:40 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* [Sat May 25 21:51:40 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 -* [Sat May 25 21:51:41 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 +* [Sun Jun 29 06:33:10 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 29 06:33:10 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 29 06:33:10 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/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:52:52 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/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 +* [Sun Jun 29 06:33:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat May 25 21:53:04 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 || : +* [Sun Jun 29 06:33:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat May 25 21:53:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sun Jun 29 06:33:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat May 25 21:53:09 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 || : +* [Sun Jun 29 06:33:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:53:10 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 || : +* [Sun Jun 29 06:33:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:53:11 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 +* [Sun Jun 29 06:33:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 @@ -8951,33 +8987,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Sat May 25 21:53:12 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 +* [Sun Jun 29 06:33:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:54:14 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 +* [Sun Jun 29 06:34:23 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.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat May 25 21:54:26 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 || : +* [Sun Jun 29 06:34:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat May 25 21:54:28 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 +* [Sun Jun 29 06:34:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat May 25 21:54:30 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 || : +* [Sun Jun 29 06:34:32 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.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:54:31 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 +* [Sun Jun 29 06:34:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 83 -* [Sat May 25 21:54:32 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* [Sat May 25 21:54:32 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 +* [Sun Jun 29 06:34:33 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 29 06:34:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Sat May 25 21:54:32 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 +* [Sun Jun 29 06:34:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Sat May 25 21:54:33 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 +* [Sun Jun 29 06:34:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* @@ -9070,7 +9106,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Sat May 25 21:54:35 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 +* [Sun Jun 29 06:34:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -9090,8 +9126,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Sat May 25 21:54:40 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 -* [Sat May 25 21:54:40 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 +* [Sun Jun 29 06:34:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:34:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0_seq2.p1, not unique enough -skipping training candidate: comp992_c0_seq2.p1, not unique enough -skipping training candidate: comp718_c0_seq2.p1, not unique enough @@ -9129,37 +9165,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Sat May 25 21:54:42 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.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 +* [Sun Jun 29 06:34:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 -* [Sat May 25 21:54:42 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 -* [Sat May 25 21:54:46 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 -* [Sat May 25 21:54:58 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 +* [Sun Jun 29 06:34:40 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 29 06:34:42 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 29 06:34:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat May 25 21:54:58 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* [Sat May 25 21:54:58 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 -* [Sat May 25 21:54:59 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 +* [Sun Jun 29 06:34:48 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 29 06:34:48 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 29 06:34:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:55:52 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.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sun Jun 29 06:35:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat May 25 21:56:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sun Jun 29 06:35:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat May 25 21:56:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sun Jun 29 06:35:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat May 25 21:56:08 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 || : +* [Sun Jun 29 06:35:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:56:09 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 || : +* [Sun Jun 29 06:35:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:56:10 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 +* [Sun Jun 29 06:35:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 @@ -9265,33 +9301,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Sat May 25 21:56:11 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 +* [Sun Jun 29 06:35:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 21:57:20 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 +* [Sun Jun 29 06:36:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat May 25 21:57:31 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 || : +* [Sun Jun 29 06:36:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat May 25 21:57:33 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 +* [Sun Jun 29 06:36:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat May 25 21:57:36 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 || : +* [Sun Jun 29 06:36:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 21:57:37 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 +* [Sun Jun 29 06:36:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 43 -* [Sat May 25 21:57:37 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* [Sat May 25 21:57:37 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 +* [Sun Jun 29 06:36:40 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 29 06:36:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Sat May 25 21:57:38 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/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 +* [Sun Jun 29 06:36:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Sat May 25 21:57:38 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/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 +* [Sun Jun 29 06:36:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* @@ -9309,31 +9345,31 @@ Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', - 'contig' => 'III', + 'asmbl' => 'comp1051_c1_seq1', 'coords' => [ [ '1642973', '1644586' ] ], - 'asmbl' => 'comp1051_c1_seq1', - 'orient' => '-', - 'gene_id' => '' + 'contig' => 'III', + 'gene_id' => '', + 'orient' => '-' }; + gene_length: 1616 + mid_pt: 808 + source: transdecoder + asmbl_id: comp1051_c1_seq1 is_3prime_partial: 0 + num_exons: 1 com_name: ORF type:5prime_partial (+),score=83.26 + is_5prime_partial: 0 + is_pseudogene: 0 strand: + - gene_type: protein-coding - gene_length: 1616 - source: transdecoder TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 - classification: annotated_genes + gene_type: protein-coding Model_feat_name: comp1051_c1_seq1.p1 - mid_pt: 808 - num_exons: 1 - is_pseudogene: 0 - asmbl_id: comp1051_c1_seq1 - is_5prime_partial: 0 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9350,8 +9386,11 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', 'contig' => 'I', + 'orient' => '-', + 'gene_id' => '', + 'trans_id' => '', + 'asmbl' => 'comp1058_c0_seq1', 'coords' => [ [ 5095548, @@ -9361,25 +9400,22 @@ 5095142, '5095301' ] - ], - 'asmbl' => 'comp1058_c0_seq1', - 'orient' => '-', - 'gene_id' => '' + ] }; - mid_pt: 248 - is_pseudogene: 0 - num_exons: 1 - asmbl_id: comp1058_c0_seq1 - is_5prime_partial: 0 - classification: annotated_genes TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + strand: + + is_5prime_partial: 0 + is_pseudogene: 0 Model_feat_name: comp1058_c0_seq1.p1 - source: transdecoder gene_type: protein-coding + com_name: ORF type:5prime_partial (+),score=32.57 + classification: annotated_genes + source: transdecoder + mid_pt: 248 gene_length: 496 + num_exons: 1 is_3prime_partial: 0 - strand: + - com_name: ORF type:5prime_partial (+),score=32.57 + asmbl_id: comp1058_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9402,10 +9438,6 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp1112_c0_seq1', - 'orient' => '-', - 'gene_id' => '', - 'trans_id' => '', 'coords' => [ [ 2380416, @@ -9416,22 +9448,26 @@ '2380336' ] ], - 'contig' => 'III' + 'trans_id' => '', + 'asmbl' => 'comp1112_c0_seq1', + 'contig' => 'III', + 'orient' => '-', + 'gene_id' => '' }; - is_5prime_partial: 0 is_pseudogene: 0 - num_exons: 1 - asmbl_id: comp1112_c0_seq1 - mid_pt: 1041 + is_5prime_partial: 0 + strand: + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 - classification: annotated_genes - Model_feat_name: comp1112_c0_seq1.p1 - gene_length: 2081 gene_type: protein-coding + Model_feat_name: comp1112_c0_seq1.p1 + com_name: ORF type:complete (+),score=155.28 + classification: annotated_genes source: transdecoder + gene_length: 2081 + mid_pt: 1041 + num_exons: 1 + asmbl_id: comp1112_c0_seq1 is_3prime_partial: 0 - com_name: ORF type:complete (+),score=155.28 - strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9453,7 +9489,6 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', 'coords' => [ [ 402195, @@ -9472,25 +9507,26 @@ '401683' ] ], + 'asmbl' => 'comp1198_c0_seq1', 'trans_id' => '', 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp1198_c0_seq1' + 'contig' => 'II' }; + num_exons: 1 + asmbl_id: comp1198_c0_seq1 + is_3prime_partial: 0 + source: transdecoder + gene_length: 597 + mid_pt: 299 classification: annotated_genes - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + gene_type: protein-coding Model_feat_name: comp1198_c0_seq1.p1 - is_5prime_partial: 0 - mid_pt: 299 is_pseudogene: 0 - asmbl_id: comp1198_c0_seq1 - num_exons: 1 - is_3prime_partial: 0 + is_5prime_partial: 0 strand: + + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 com_name: ORF type:internal (+),score=37.56 - source: transdecoder - gene_type: protein-coding - gene_length: 597 gene_synonyms: mRNA_coords CDS_coords @@ -9518,9 +9554,6 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'orient' => '-', - 'asmbl' => 'comp1210_c0_seq1', 'coords' => [ [ 368840, @@ -9531,23 +9564,26 @@ '368790' ] ], + 'trans_id' => '', + 'asmbl' => 'comp1210_c0_seq1', 'contig' => 'III', - 'trans_id' => '' + 'orient' => '-', + 'gene_id' => '' }; - mid_pt: 777 - num_exons: 1 - is_pseudogene: 0 - asmbl_id: comp1210_c0_seq1 is_5prime_partial: 0 - classification: annotated_genes + is_pseudogene: 0 + strand: + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + gene_type: protein-coding Model_feat_name: comp1210_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=12.16 + classification: annotated_genes source: transdecoder - gene_type: protein-coding gene_length: 1554 + mid_pt: 777 + num_exons: 1 + asmbl_id: comp1210_c0_seq1 is_3prime_partial: 0 - strand: + - com_name: ORF type:5prime_partial (+),score=12.16 gene_synonyms: mRNA_coords CDS_coords @@ -9578,26 +9614,26 @@ '3841303' ] ], - 'contig' => 'II', 'trans_id' => '', - 'gene_id' => '', + 'asmbl' => 'comp366_c0_seq1', + 'contig' => 'II', 'orient' => '-', - 'asmbl' => 'comp366_c0_seq1' + 'gene_id' => '' }; - Model_feat_name: comp366_c0_seq1.p1 - classification: annotated_genes - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - is_5prime_partial: 0 mid_pt: 170 - num_exons: 1 - is_pseudogene: 0 + gene_length: 340 + source: transdecoder + is_3prime_partial: 0 asmbl_id: comp366_c0_seq1 - strand: - + num_exons: 1 com_name: ORF type:internal (-),score=12.83 - is_3prime_partial: 0 - source: transdecoder + strand: - + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + is_pseudogene: 0 + is_5prime_partial: 0 gene_type: protein-coding - gene_length: 340 + Model_feat_name: comp366_c0_seq1.p1 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9623,32 +9659,32 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'I', + 'trans_id' => '', + 'asmbl' => 'comp610_c0_seq1', 'coords' => [ [ '5471264', '5472770' ] ], - 'trans_id' => '', + 'contig' => 'I', 'gene_id' => '', - 'asmbl' => 'comp610_c0_seq1', 'orient' => '-' }; - gene_type: protein-coding - gene_length: 1509 - source: transdecoder + classification: annotated_genes com_name: ORF type:5prime_partial (+),score=50.55 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 strand: + + is_5prime_partial: 0 + is_pseudogene: 0 + Model_feat_name: comp610_c0_seq1.p1 + gene_type: protein-coding is_3prime_partial: 0 - mid_pt: 755 asmbl_id: comp610_c0_seq1 - is_pseudogene: 0 num_exons: 1 - is_5prime_partial: 0 - Model_feat_name: comp610_c0_seq1.p1 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - classification: annotated_genes + mid_pt: 755 + gene_length: 1509 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9667,32 +9703,32 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'orient' => '-', - 'asmbl' => 'comp645_c0_seq1', 'contig' => 'I', + 'orient' => '-', + 'gene_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], - 'trans_id' => '' + 'trans_id' => '', + 'asmbl' => 'comp645_c0_seq1' }; classification: annotated_genes TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 - Model_feat_name: comp645_c0_seq1.p1 + strand: + is_5prime_partial: 0 is_pseudogene: 0 - asmbl_id: comp645_c0_seq1 + Model_feat_name: comp645_c0_seq1.p1 + gene_type: protein-coding + com_name: ORF type:5prime_partial (+),score=273.35 num_exons: 1 - mid_pt: 1827 is_3prime_partial: 0 - strand: + - com_name: ORF type:5prime_partial (+),score=273.35 + asmbl_id: comp645_c0_seq1 source: transdecoder + mid_pt: 1827 gene_length: 3653 - gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9708,7 +9744,9 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'orient' => '+', + 'gene_id' => '', + 'contig' => 'II', 'coords' => [ [ 380308, @@ -9719,25 +9757,23 @@ '381243' ] ], - 'contig' => 'II', 'asmbl' => 'comp688_c0_seq1', - 'orient' => '+', - 'gene_id' => '' + 'trans_id' => '' }; - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 - classification: annotated_genes + com_name: ORF type:complete (+),score=172.54 + gene_type: protein-coding Model_feat_name: comp688_c0_seq1.p1 is_5prime_partial: 0 - asmbl_id: comp688_c0_seq1 is_pseudogene: 0 - num_exons: 1 - mid_pt: 1392 - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=172.54 strand: + + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + classification: annotated_genes gene_length: 2784 - gene_type: protein-coding + mid_pt: 1392 source: transdecoder + asmbl_id: comp688_c0_seq1 + is_3prime_partial: 0 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9761,6 +9797,7 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'asmbl' => 'comp856_c0_seq1', 'trans_id' => '', 'coords' => [ [ @@ -9772,25 +9809,24 @@ '3755057' ] ], - 'contig' => 'II', - 'asmbl' => 'comp856_c0_seq1', 'orient' => '+', - 'gene_id' => '' + 'gene_id' => '', + 'contig' => 'II' }; - mid_pt: 785 - is_pseudogene: 0 - asmbl_id: comp856_c0_seq1 - num_exons: 1 - is_5prime_partial: 0 - classification: annotated_genes + com_name: ORF type:complete (+),score=71.94 TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + strand: + + is_5prime_partial: 0 + is_pseudogene: 0 Model_feat_name: comp856_c0_seq1.p1 - source: transdecoder gene_type: protein-coding + classification: annotated_genes + mid_pt: 785 gene_length: 1569 + source: transdecoder is_3prime_partial: 0 - strand: + - com_name: ORF type:complete (+),score=71.94 + asmbl_id: comp856_c0_seq1 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9810,7 +9846,8 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', + 'asmbl' => 'comp873_c0_seq2', + 'trans_id' => '', 'coords' => [ [ 3727877, @@ -9825,24 +9862,23 @@ '3727657' ] ], - 'trans_id' => '', 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp873_c0_seq2' + 'contig' => 'II' }; - gene_type: protein-coding - gene_length: 1025 source: transdecoder - com_name: ORF type:5prime_partial (+),score=8.59 - strand: + - is_3prime_partial: 0 + gene_length: 1025 mid_pt: 513 - is_pseudogene: 0 - asmbl_id: comp873_c0_seq2 num_exons: 1 + asmbl_id: comp873_c0_seq2 + is_3prime_partial: 0 is_5prime_partial: 0 - Model_feat_name: comp873_c0_seq2.p1 + is_pseudogene: 0 TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + strand: + + Model_feat_name: comp873_c0_seq2.p1 + gene_type: protein-coding + com_name: ORF type:5prime_partial (+),score=8.59 classification: annotated_genes gene_synonyms: mRNA_coords @@ -9867,9 +9903,11 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'contig' => 'III', 'gene_id' => '', - 'asmbl' => 'comp888_c0_seq1', 'orient' => '-', + 'trans_id' => '', + 'asmbl' => 'comp888_c0_seq1', 'coords' => [ [ 1268244, @@ -9879,24 +9917,22 @@ 1267938, '1268172' ] - ], - 'contig' => 'III', - 'trans_id' => '' + ] }; - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 + asmbl_id: comp888_c0_seq1 + is_3prime_partial: 0 + num_exons: 1 + gene_length: 589 + mid_pt: 295 + source: transdecoder classification: annotated_genes + com_name: ORF type:5prime_partial (+),score=23.94 + gene_type: protein-coding Model_feat_name: comp888_c0_seq1.p1 is_pseudogene: 0 - num_exons: 1 - asmbl_id: comp888_c0_seq1 - mid_pt: 295 is_5prime_partial: 0 - is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=23.94 strand: + - gene_length: 589 - gene_type: protein-coding - source: transdecoder + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9919,7 +9955,7 @@ Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', - 'contig' => 'III', + 'asmbl' => 'comp940_c0_seq1', 'coords' => [ [ 105641, @@ -9930,24 +9966,24 @@ '106404' ] ], - 'asmbl' => 'comp940_c0_seq1', + 'contig' => 'III', 'orient' => '+', 'gene_id' => '' }; + num_exons: 1 + asmbl_id: comp940_c0_seq1 is_3prime_partial: 0 - strand: + - com_name: ORF type:complete (+),score=94.37 source: transdecoder gene_length: 2129 - gene_type: protein-coding + mid_pt: 1065 classification: annotated_genes + is_5prime_partial: 0 + is_pseudogene: 0 TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + strand: + Model_feat_name: comp940_c0_seq1.p1 - is_pseudogene: 0 - num_exons: 1 - asmbl_id: comp940_c0_seq1 - mid_pt: 1065 - is_5prime_partial: 0 + gene_type: protein-coding + com_name: ORF type:complete (+),score=94.37 gene_synonyms: mRNA_coords CDS_coords @@ -9968,6 +10004,10 @@ Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'contig' => 'I', + 'gene_id' => '', + 'orient' => '-', + 'trans_id' => '', + 'asmbl' => 'comp983_c0_seq1', 'coords' => [ [ 4100066, @@ -9977,26 +10017,22 @@ 4098246, '4100014' ] - ], - 'trans_id' => '', - 'gene_id' => '', - 'asmbl' => 'comp983_c0_seq1', - 'orient' => '-' + ] }; - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 - classification: annotated_genes - Model_feat_name: comp983_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=143.65 is_5prime_partial: 0 is_pseudogene: 0 - asmbl_id: comp983_c0_seq1 - num_exons: 1 - mid_pt: 935 - is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=143.65 strand: + - gene_length: 1870 + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 gene_type: protein-coding + Model_feat_name: comp983_c0_seq1.p1 + classification: annotated_genes + gene_length: 1870 + mid_pt: 935 source: transdecoder + asmbl_id: comp983_c0_seq1 + is_3prime_partial: 0 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -10040,7 +10076,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Sat May 25 21:57:43 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 +* [Sun Jun 29 06:36:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -10065,8 +10101,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Sat May 25 21:58:14 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 -* [Sat May 25 21:58:15 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 +* [Sun Jun 29 06:36:55 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 29 06:36:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -12684,37 +12720,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Sat May 25 21:58:20 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 +* [Sun Jun 29 06:36:58 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Sat May 25 21:58:20 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 -* [Sat May 25 21:58:27 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Sat May 25 21:59:47 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 +* [Sun Jun 29 06:36:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:37:01 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 29 06:37:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat May 25 21:59:48 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* [Sat May 25 21:59:48 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 -* [Sat May 25 21:59:51 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 +* [Sun Jun 29 06:37:34 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 29 06:37:34 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 29 06:37:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 22:00:47 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 +* [Sun Jun 29 06:38:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat May 25 22:01:00 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 || : +* [Sun Jun 29 06:38:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat May 25 22:01:02 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 +* [Sun Jun 29 06:38:14 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat May 25 22:01:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sun Jun 29 06:38:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:01:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Sun Jun 29 06:38:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:01:06 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/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 +* [Sun Jun 29 06:38:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 336 num_incorporate: 100 -feature swap of score: 3.78911079353454 instead of -4.15762669956 -feature swap of score: 4.3075564869904 instead of -3.54241712691985 @@ -12775,7 +12811,7 @@ -feature swap of score: 3.99301668862372 instead of 1.24561259795263 -feature swap of score: 1.72372236527001 instead of 1.02241527158741 -feature swap of score: 6.86300883201794 instead of 1.14563582053961 --feature swap of score: 5.54190533772704 instead of 1.28297492173033 +-feature swap of score: 5.54190533772704 instead of 1.28297492173032 -feature swap of score: 2.51308026289154 instead of 1.4180584754329 -feature swap of score: 3.38846514773249 instead of 1.2857641622143 -feature swap of score: 2.49385651598659 instead of 1.55130322997112 @@ -12817,33 +12853,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Sat May 25 22:01:07 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 +* [Sun Jun 29 06:38:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 22:02:16 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 +* [Sun Jun 29 06:38:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat May 25 22:02:27 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 || : +* [Sun Jun 29 06:38:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat May 25 22:02:29 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 +* [Sun Jun 29 06:38:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat May 25 22:02:31 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 || : +* [Sun Jun 29 06:38:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:02:33 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 +* [Sun Jun 29 06:38:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 -* [Sat May 25 22:02:36 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* [Sat May 25 22:02:36 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 +* [Sun Jun 29 06:38:55 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 29 06:38:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Sat May 25 22:02:36 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 +* [Sun Jun 29 06:38:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Sat May 25 22:02:40 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/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 +* [Sun Jun 29 06:38:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* @@ -12955,7 +12991,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Sat May 25 22:02:56 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 +* [Sun Jun 29 06:39:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -12979,58 +13015,58 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Sat May 25 22:02:59 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 -* [Sat May 25 22:03:00 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_i3.p1, not unique enough +* [Sun Jun 29 06:39:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:39:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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_i4.p1, not unique enough -skipping training candidate: bdg_i1.p1, not unique enough -skipping training candidate: Dgk_i7.p1, not unique enough -skipping training candidate: Cdep_i1.p1, not unique enough -skipping training candidate: eIF5B_i2.p1, not unique enough --skipping training candidate: eIF5B_i3.p1, not unique enough +-skipping training candidate: eIF5B_i4.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough --skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: Dgk_i3.p1, not unique enough +-skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i3.p1, not unique enough +-skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough --skipping training candidate: Calx_i1.p1, not unique enough --skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: Calx_i4.p1, not unique enough +-skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i5.p1, not unique enough +-skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough --skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough --skipping training candidate: Klp10A_i3.p1, not unique enough +-skipping training candidate: CG8312_i2.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: Klp10A_i4.p1, not unique enough +-skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: Klp10A_i5.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_i4.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_i1.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_i2.p1, not unique enough --skipping training candidate: hrg_i3.p1, not unique enough +-skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: 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 @@ -13043,8 +13079,8 @@ -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough --skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough +-skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Est-6_i2.p1, not unique enough @@ -13052,34 +13088,34 @@ -skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough --skipping training candidate: CG30438_i3.p1, not unique enough +-skipping training candidate: CG30438_i5.p1, not unique enough -skipping training candidate: CG30438_i2.p1, not unique enough --skipping training candidate: CG30438_i1.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_i3.p1, not unique enough -skipping training candidate: Eno_i4.p1, not unique enough --skipping training candidate: Eno_i1.p1, not unique enough +-skipping training candidate: Eno_i5.p1, not unique enough +-skipping training candidate: Eno_i3.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough --skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i7.p1, not unique enough --skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_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_i10.p1, not unique enough -skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough --skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough +-skipping training candidate: Eno_i1.p2, not unique enough +-skipping training candidate: Eno_i6.p1, not unique enough +-skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough --skipping training candidate: Eno_i4.p2, not unique enough --skipping training candidate: Eno_i6.p1, not unique enough --skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: CG6424_i3.p2, not unique enough -skipping training candidate: CG6424_i1.p2, not unique enough -skipping training candidate: CG6424_i4.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough @@ -13089,24 +13125,24 @@ -skipping training candidate: Irk2_i4.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i2.p1, not unique enough -skipping training candidate: AdipoR_i5.p1, not unique enough +-skipping training candidate: AdipoR_i2.p1, not unique enough -skipping training candidate: AdipoR_i4.p1, not unique enough --skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough +-skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough -skipping training candidate: kto_i1.p2, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough --skipping training candidate: nmo_i3.p1, not unique enough -skipping training candidate: nmo_i1.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough --skipping training candidate: CG8136_i1.p1, not unique enough +-skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough --skipping training candidate: CG7564_i4.p1, not unique enough --skipping training candidate: CG7564_i3.p1, not unique enough -skipping training candidate: CG7564_i2.p3, not unique enough +-skipping training candidate: CG7564_i1.p1, not unique enough +-skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough -skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough @@ -13118,11 +13154,11 @@ -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough --skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: ogre_i4.p1, not unique enough --skipping training candidate: ogre_i6.p1, not unique enough --skipping training candidate: ogre_i2.p1, not unique enough -skipping training candidate: ogre_i1.p1, not unique enough +-skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough +-skipping training candidate: ogre_i6.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 @@ -13132,71 +13168,71 @@ -skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: sqd_i4.p1, 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: Klp10A_i4.p2, not unique enough +-skipping training candidate: Klp10A_i3.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: Calx_i7.p2, not unique enough --skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough +-skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough -skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough --skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough +-skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i4.p1, not unique enough --skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough +-skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough -skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: l(3)05822_i2.p2, not unique enough --skipping training candidate: Tm1_i6.p1, not unique enough --skipping training candidate: Tm1_i9.p1, not unique enough +-skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i11.p1, not unique enough --skipping training candidate: Tm1_i2.p1, not unique enough -skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Tm1_i3.p1, not unique enough +-skipping training candidate: Tm1_i2.p1, not unique enough +-skipping training candidate: Tm1_i9.p1, not unique enough +-skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Npl4_i3.p2, not unique enough -skipping training candidate: Npl4_i2.p2, not unique enough --skipping training candidate: Npl4_i1.p2, not unique enough --skipping training candidate: Sec16_i1.p2, not unique enough --skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough --skipping training candidate: CG8312_i2.p2, not unique enough +-skipping training candidate: Sec16_i5.p2, not unique enough +-skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough +-skipping training candidate: CG8312_i2.p2, not unique enough -skipping training candidate: Dgk_i7.p2, not unique enough -skipping training candidate: eIF5B_i2.p2, not unique enough --skipping training candidate: eIF5B_i5.p2, not unique enough +-skipping training candidate: eIF5B_i4.p2, not unique enough -skipping training candidate: eIF5B_i1.p2, not unique enough --skipping training candidate: eIF5B_i3.p2, not unique enough --skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: Dgk_i3.p2, not unique enough +-skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: Dgk_i2.p2, not unique enough -skipping training candidate: l(1)G0193_i1.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough --skipping training candidate: Dgk_i2.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_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_i1.p3, not unique enough -skipping training candidate: l(3)05822_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i1.p2, not unique enough +-skipping training candidate: Sec16_i6.p2, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: Sec16_i2.p3, not unique enough --skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG13887_i2.p1, not unique enough -skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough --skipping training candidate: nmo_i3.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough --skipping training candidate: nmo_i6.p2, not unique enough -skipping training candidate: nmo_i2.p2, not unique enough +-skipping training candidate: nmo_i1.p2, not unique enough +-skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough -skipping training candidate: nmo_i5.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough @@ -13208,295 +13244,295 @@ -skipping training candidate: gukh_i1.p2, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough +-skipping training candidate: RpL15_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_i5.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough --skipping training candidate: RpL15_i3.p1, not unique enough --skipping training candidate: RpL15_i1.p1, not unique enough +-skipping training candidate: Npl4_i3.p3, not unique enough -skipping training candidate: Npl4_i2.p3, not unique enough --skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: trc_i2.p2, not unique enough --skipping training candidate: Hsc70-1_i3.p3, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough +-skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough --skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough --skipping training candidate: CG10237_i2.p2, not unique enough --skipping training candidate: CG10237_i5.p2, not unique enough +-skipping training candidate: CG14995_i4.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: Eno_i3.p3, not unique enough --skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i4.p3, not unique enough +-skipping training candidate: CG10237_i3.p2, not unique enough -skipping training candidate: Eno_i6.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: Eno_i4.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_i3.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_i7.p3, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough --skipping training candidate: gukh_i2.p2, not unique enough +-skipping training candidate: gukh_i1.p3, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough -skipping training candidate: ATPsyn-d_i3.p1, not unique enough --skipping training candidate: CG10082_i1.p2, not unique enough +-skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough --skipping training candidate: CG30438_i3.p2, not unique enough --skipping training candidate: CG30438_i2.p2, not unique enough --skipping training candidate: CG30438_i1.p2, not unique enough +-skipping training candidate: CG30438_i5.p2, not unique enough -skipping training candidate: CG30438_i4.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_i4.p3, not unique enough +-skipping training candidate: cdi_i1.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough +-skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CanB2_i1.p1, not unique enough -skipping training candidate: ADD1_i2.p2, not unique enough --skipping training candidate: Sec16_i4.p4, not unique enough -skipping training candidate: Sec16_i3.p3, not unique enough +-skipping training candidate: Sec16_i1.p4, not unique enough -skipping training candidate: bic_i1.p1, not unique enough --skipping training candidate: CG12581_i1.p2, 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_i1.p1, not unique enough --skipping training candidate: ctp_i3.p1, not unique enough +-skipping training candidate: ctp_i4.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: hrg_i3.p2, not unique enough --skipping training candidate: Eno_i3.p4, not unique enough --skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: hrg_i4.p2, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Eno_i1.p4, not unique enough --skipping training candidate: Klp10A_i3.p3, not unique enough +-skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough +-skipping training candidate: Eno_i5.p4, not unique enough +-skipping training candidate: Eno_i3.p4, not unique enough -skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough --skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i2.p4, not unique enough --skipping training candidate: Calx_i2.p2, not unique enough --skipping training candidate: Calx_i8.p2, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough +-skipping training candidate: Klp10A_i5.p3, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough -skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i3.p2, not unique enough --skipping training candidate: Calx_i5.p2, not unique enough -skipping training candidate: Calx_i9.p2, not unique enough +-skipping training candidate: Calx_i6.p2, not unique enough +-skipping training candidate: Calx_i1.p2, not unique enough +-skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Calx_i5.p2, not unique enough +-skipping training candidate: Calx_i2.p2, not unique enough +-skipping training candidate: CG7564_i2.p4, not unique enough +-skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough +-skipping training candidate: CG7564_i1.p3, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough --skipping training candidate: CG7564_i2.p4, not unique enough --skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: Gale_i2.p2, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough --skipping training candidate: eIF5B_i5.p3, not unique enough +-skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: eIF5B_i1.p3, not unique enough --skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: eIF5B_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_i2.p3, 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: CG6424_i4.p3, not unique enough --skipping training candidate: Tm1_i5.p2, not unique enough -skipping training candidate: Tm1_i16.p2, not unique enough --skipping training candidate: Tm1_i14.p2, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Tm1_i13.p2, not unique enough +-skipping training candidate: Tm1_i5.p2, not unique enough -skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Dgk_i2.p5, not unique enough -skipping training candidate: Dgk_i7.p5, not unique enough --skipping training candidate: cdi_i2.p3, not unique enough +-skipping training candidate: cdi_i1.p4, not unique enough -skipping training candidate: eff_i2.p1, not unique enough -skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough --skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: eIF5B_i4.p5, not unique enough -skipping training candidate: eIF5B_i1.p4, not unique enough --skipping training candidate: eIF5B_i3.p4, not unique enough --skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: Sec16_i6.p3, not unique enough -skipping training candidate: Sec16_i5.p4, not unique enough --skipping training candidate: Sec16_i2.p5, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough -skipping training candidate: Sec16_i3.p4, not unique enough --skipping training candidate: CG32082_i3.p2, not unique enough --skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough +-skipping training candidate: CG32082_i3.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_i7.p6, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: l(3)05822_i2.p4, not unique enough --skipping training candidate: sqd_i2.p2, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough +-skipping training candidate: sqd_i1.p2, not unique enough -skipping training candidate: CG7564_i2.p6, not unique enough +-skipping training candidate: CG7564_i1.p4, not unique enough +-skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough -skipping training candidate: S-Lap3_i2.p2, not unique enough --skipping training candidate: cdi_i2.p4, not unique enough +-skipping training candidate: cdi_i1.p5, not unique enough -skipping training candidate: CG6091_i1.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_i1.p2, not unique enough --skipping training candidate: Cnx99A_i2.p2, not unique enough +-skipping training candidate: Cnx99A_i4.p2, not unique enough -skipping training candidate: Cnx99A_i3.p2, not unique enough --skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: Cnx99A_i2.p2, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough -skipping training candidate: Sec16_i3.p5, not unique enough +-skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: 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: hrg_i3.p3, not unique enough +-skipping training candidate: hrg_i1.p3, not unique enough -skipping training candidate: ATPsyn-d_i3.p2, not unique enough -skipping training candidate: CG6091_i1.p3, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough --skipping training candidate: CG33970_i2.p2, not unique enough -skipping training candidate: CG33970_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough --skipping training candidate: eIF5B_i1.p5, not unique enough +-skipping training candidate: CG33970_i2.p2, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough --skipping training candidate: Aldh-III_i10.p2, not unique enough +-skipping training candidate: eIF5B_i1.p5, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: Aldh-III_i8.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: CG13284_i4.p2, not unique enough -skipping training candidate: CG13284_i1.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_i2.p7, 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_i1.p5, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Dgk_i2.p7, not unique enough -skipping training candidate: Dgk_i7.p7, not unique enough --skipping training candidate: Tm1_i5.p3, not unique enough +-skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Tm1_i16.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_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough +-skipping training candidate: Tm1_i13.p3, not unique enough +-skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: CG8312_i4.p3, not unique enough -skipping training candidate: CG8312_i4.p4, not unique enough --skipping training candidate: Klp10A_i3.p4, not unique enough +-skipping training candidate: CG8312_i2.p3, not unique enough +-skipping training candidate: CG8312_i2.p4, not unique enough +-skipping training candidate: CG8312_i3.p3, not unique enough +-skipping training candidate: CG8312_i3.p4, not unique enough -skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough --skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i5.p4, not unique enough -skipping training candidate: eff_i2.p2, not unique enough -skipping training candidate: eff_i3.p2, 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_i7.p4, not unique enough --skipping training candidate: CG14995_i3.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: CG6424_i2.p4, not unique enough +-skipping training candidate: CG14995_i3.p4, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough -skipping training candidate: CG6424_i4.p4, not unique enough --skipping training candidate: CG12581_i1.p3, not unique enough --skipping training candidate: CG32082_i3.p3, not unique enough --skipping training candidate: CG32082_i1.p3, not unique enough +-skipping training candidate: CG12581_i2.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_i2.p3, not unique enough +-skipping training candidate: CG32082_i3.p3, not unique enough -skipping training candidate: Cnx99A_i3.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p3, not unique enough +-skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough --skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough --skipping training candidate: CG33970_i2.p3, not unique enough -skipping training candidate: CG33970_i1.p3, not unique enough --skipping training candidate: Sec16_i1.p7, not unique enough +-skipping training candidate: CG33970_i2.p3, not unique enough +-skipping training candidate: Sec16_i6.p5, not unique enough -skipping training candidate: Sec16_i5.p6, not unique enough --skipping training candidate: Sec16_i2.p7, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough -skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: Sec16_i1.p7, 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_i2.p2, not unique enough -skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i2.p4, not unique enough -skipping training candidate: Cnx99A_i3.p4, not unique enough --skipping training candidate: CG13887_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i2.p4, not unique enough -skipping training candidate: CG13887_i4.p2, not unique enough --skipping training candidate: CG6145_i5.p2, not unique enough --skipping training candidate: CG6145_i1.p2, not unique enough --skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG13887_i2.p2, not unique enough -skipping training candidate: CG6145_i3.p2, not unique enough --skipping training candidate: Calx_i2.p3, not unique enough --skipping training candidate: Calx_i8.p3, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: CG6145_i4.p2, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough -skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i3.p3, not unique enough --skipping training candidate: Calx_i5.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: mge_i2.p2, not unique enough +-skipping training candidate: Calx_i6.p3, not unique enough +-skipping training candidate: Calx_i1.p3, not unique enough +-skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: Calx_i5.p3, not unique enough +-skipping training candidate: Calx_i2.p3, not unique enough +-skipping training candidate: mge_i1.p2, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_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_i7.p2, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough --skipping training candidate: Aldh-III_i9.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough +-skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: Aldh-III_i2.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough +-skipping training candidate: Aldh-III_i6.p2, not unique enough +-skipping training candidate: Cdep_i4.p3, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough --skipping training candidate: Cdep_i2.p9, not unique enough -skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough --skipping training candidate: hrg_i3.p4, not unique enough +-skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: CG33125_i2.p2, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough --skipping training candidate: CG12581_i1.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: CG12581_i2.p4, not unique enough +-skipping training candidate: Sec16_i6.p6, not unique enough +-skipping training candidate: Sec16_i6.p7, not unique enough -skipping training candidate: Sec16_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough --skipping training candidate: Sec16_i2.p8, not unique enough --skipping training candidate: Sec16_i2.p9, not unique enough -skipping training candidate: Sec16_i4.p8, not unique enough -skipping training candidate: Sec16_i4.p9, not unique enough -skipping training candidate: Sec16_i3.p7, not unique enough -skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i1.p8, not unique enough +-skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough -skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_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_i3.p5, not unique enough +-skipping training candidate: IP3K1_i1.p3, not unique enough -skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough --skipping training candidate: Klp10A_i4.p5, not unique enough +-skipping training candidate: Klp10A_i3.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: 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_i1.p5, not unique enough --skipping training candidate: Cdep_i2.p10, not unique enough -skipping training candidate: Est-6_i2.p2, 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: Klp10A_i4.p6, not unique enough +-skipping training candidate: Klp10A_i3.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: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i1.p5, not unique enough --skipping training candidate: Cnx99A_i2.p5, not unique enough +-skipping training candidate: Cnx99A_i4.p3, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough +-skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Myo61F_i1.p3, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough -skipping training candidate: Myo61F_i3.p3, not unique enough @@ -13504,170 +13540,175 @@ -skipping training candidate: Myo61F_i2.p4, not unique enough -skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: bic_i1.p3, not unique enough --skipping training candidate: CG10082_i1.p5, not unique enough --skipping training candidate: CG32082_i3.p4, not unique enough --skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: CG10082_i2.p3, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: Eno_i3.p5, not unique enough --skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: CG32082_i3.p4, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough --skipping training candidate: Eno_i1.p6, not unique enough --skipping training candidate: Sec16_i1.p10, not unique enough +-skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough +-skipping training candidate: Eno_i5.p6, not unique enough +-skipping training candidate: Eno_i3.p5, 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_i2.p8, not unique enough +-skipping training candidate: Sec16_i1.p10, not unique enough +-skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough +-skipping training candidate: Dgk_i2.p8, not unique enough -skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Dgk_i5.p5, not unique enough -skipping training candidate: nmo_i6.p3, not unique enough --skipping training candidate: CG33970_i1.p4, not unique enough --skipping training candidate: sqd_i3.p2, not unique enough +-skipping training candidate: CG33970_i2.p5, not unique enough +-skipping training candidate: sqd_i5.p3, not unique enough -skipping training candidate: Dgk_i1.p7, not unique enough --skipping training candidate: Dgk_i3.p7, not unique enough +-skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: His4r_i3.p1, not unique enough --skipping training candidate: His4r_i2.p1, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough --skipping training candidate: Hsc70-1_i3.p4, not unique enough +-skipping training candidate: His4r_i1.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: hrg_i4.p6, not unique enough --skipping training candidate: hrg_i3.p5, not unique enough --skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: CG8136_i2.p2, not unique enough +-skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: CG8136_i4.p2, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough -skipping training candidate: Myo61F_i1.p5, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough -skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough -skipping training candidate: CG6091_i3.p5, not unique enough --skipping training candidate: CG6145_i5.p3, not unique enough --skipping training candidate: CG6145_i1.p3, not unique enough --skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i3.p3, not unique enough --skipping training candidate: gukh_i2.p3, not unique enough --skipping training candidate: sqd_i3.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: CG6145_i4.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: CG33125_i2.p3, not unique enough --skipping training candidate: gukh_i2.p4, not unique enough +-skipping training candidate: gukh_i1.p5, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Sat May 25 22:03:00 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 +* [Sun Jun 29 06:39:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 49.4 -* [Sat May 25 22:03:00 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 -* [Sat May 25 22:03:02 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 -* [Sat May 25 22:03:14 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 +* [Sun Jun 29 06:39:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 29 06:39:08 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 29 06:39:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Sat May 25 22:03:15 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* [Sat May 25 22:03:15 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 -* [Sat May 25 22:03:16 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 +* [Sun Jun 29 06:39:13 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 29 06:39:13 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 29 06:39:14 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 22:04:18 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/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 +* [Sun Jun 29 06:39:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Sat May 25 22:04:30 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 || : +* [Sun Jun 29 06:39:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Sat May 25 22:04:32 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 +* [Sun Jun 29 06:39:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Sat May 25 22:04:34 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 || : +* [Sun Jun 29 06:39:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:04:35 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 || : +* [Sun Jun 29 06:39:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:04:36 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 +* [Sun Jun 29 06:39:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 253 num_incorporate: 75 --feature swap of score: -1.36422091174318 instead of -3.50457693057379 --feature swap of score: -1.27876344796099 instead of -3.41529506164057 --feature swap of score: -2.01185983133209 instead of -3.12420913559554 --feature swap of score: -1.48920617497343 instead of -1.61191063226039 --feature swap of score: -0.977230770550059 instead of -1.42777098974194 --feature swap of score: -0.616418900587045 instead of -1.47763106468985 --feature swap of score: 2.00232593628017 instead of -1.15070424122836 --feature swap of score: -0.535632116520219 instead of -1.06553078374592 --feature swap of score: -2.32898998148547 instead of -2.39772067085693 --feature swap of score: 2.53494312587293 instead of -1.24613970409572 --feature swap of score: 1.99483162907706 instead of -1.47101539624722 --feature swap of score: -0.984904405929157 instead of -1.11183927840374 --feature swap of score: -0.472590659976243 instead of -1.04418178303793 --feature swap of score: -0.00912440426309791 instead of -1.11973381538235 --feature swap of score: 1.11807744881573 instead of -0.799362841578421 --feature swap of score: 2.11276281923091 instead of -1.03917722962427 --feature swap of score: -0.703892338618411 instead of -1.09720496435706 --feature swap of score: 1.40031687577617 instead of -0.991774452181312 --feature swap of score: -0.533403537248485 instead of -0.890217066547064 --feature swap of score: 0.309820691310281 instead of -0.750921389067211 --feature swap of score: 0.52332384206526 instead of -0.934862980946392 --feature swap of score: 3.17472724788169 instead of -0.715564568900977 --feature swap of score: 1.88735658843832 instead of -0.592992796149177 --feature swap of score: 0.14874442197923 instead of -0.636657416949876 --feature swap of score: 2.39383415258012 instead of -0.68054838844956 --feature swap of score: 0.128123942899117 instead of -0.301462193336326 --feature swap of score: 1.50626325706672 instead of -0.205712026648554 --feature swap of score: 1.39897303077279 instead of -0.387491245245141 --feature swap of score: 0.788235286535452 instead of -0.111060943059932 --feature swap of score: 2.54021699767812 instead of -0.280424737301337 --feature swap of score: 0.212562716778611 instead of 0.00937678216881982 --feature swap of score: 0.356435327285008 instead of -0.135133445701888 --feature swap of score: -0.00964277673461839 instead of -0.196422946963689 --feature swap of score: -0.00506643082004649 instead of -0.29506306775421 --feature swap of score: 1.8095102591395 instead of -0.191241434226663 --feature swap of score: 0.607602203817987 instead of -0.151966341275834 --feature swap of score: 2.74271579663183 instead of -0.492044782745226 --feature swap of score: 0.423505890150341 instead of -0.39635068149932 --feature swap of score: 1.65585791971248 instead of 0.081616384764277 --feature swap of score: 0.346624878764665 instead of 0.10767555604494 --feature swap of score: 2.13485177144241 instead of 0.225332953847482 --feature swap of score: 0.376502422396273 instead of -1.02051109388978 --feature swap of score: 0.354385352031989 instead of 0.071487416172058 --feature swap of score: 2.08057568040781 instead of -0.0209127854199098 --feature swap of score: 1.62882740700499 instead of -0.307324856854348 --feature swap of score: 3.02415122832039 instead of 0.286956163823837 --feature swap of score: 1.08451470773481 instead of 0.579263170409803 --feature swap of score: 2.69455402511026 instead of 0.076713413303272 --feature swap of score: 2.00591773898152 instead of 0.144107040747365 --feature swap of score: 3.18769993507827 instead of 0.335490508722978 --feature swap of score: 4.87369670505148 instead of 0.314686242853829 --feature swap of score: 1.08795812509787 instead of 0.376687489375721 --feature swap of score: 5.8267218084514 instead of 0.52785926061855 --feature swap of score: 3.52532163838375 instead of 0.565073797628557 --num feature swaps: 54 -* [Sat May 25 22:04:36 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 +-feature swap of score: -1.09356878127237 instead of -3.53518410052991 +-feature swap of score: -1.55532505728465 instead of -3.26137379452671 +-feature swap of score: -1.5958563807238 instead of -2.65564352052324 +-feature swap of score: -1.37685526837281 instead of -1.63989807063546 +-feature swap of score: -0.838405384711912 instead of -1.26631811643239 +-feature swap of score: -0.767392698487935 instead of -1.07144489759151 +-feature swap of score: 2.0873032869115 instead of -0.854802408475146 +-feature swap of score: -0.60480657507311 instead of -0.94270191509216 +-feature swap of score: 2.86040175884911 instead of -0.97333725582326 +-feature swap of score: -0.340064638652807 instead of -0.808103029231306 +-feature swap of score: -1.93643775537634 instead of -2.06459912803986 +-feature swap of score: 2.43595375830424 instead of -1.41213756094892 +-feature swap of score: -0.910387331015829 instead of -1.49328160968964 +-feature swap of score: 0.547570587441442 instead of -1.40487249382285 +-feature swap of score: 1.16778421812456 instead of -1.28781455753434 +-feature swap of score: 1.5027887115833 instead of -0.995229037576642 +-feature swap of score: -1.15320132123816 instead of -1.28979897020018 +-feature swap of score: -0.297517595375679 instead of -1.13096522883084 +-feature swap of score: -0.448763493965108 instead of -1.26548135802896 +-feature swap of score: -0.131837467512283 instead of -1.21163098652144 +-feature swap of score: -0.264748449392398 instead of -1.05334282416112 +-feature swap of score: 0.960149728034013 instead of -0.403916598496551 +-feature swap of score: 3.48604277212379 instead of -0.432043532076316 +-feature swap of score: 1.03993506387852 instead of -0.488836139079602 +-feature swap of score: -0.233262093692731 instead of -0.787647855703714 +-feature swap of score: 2.91097472927971 instead of -0.801552491861535 +-feature swap of score: -0.710654059629773 instead of -0.878817438860577 +-feature swap of score: 0.372751483655579 instead of -0.321386534948643 +-feature swap of score: 1.58626800093113 instead of -0.267274901499907 +-feature swap of score: 1.14126370355385 instead of -0.236762506310179 +-feature swap of score: 0.375200856356846 instead of -0.240323122364946 +-feature swap of score: -0.442228192672869 instead of -0.445975260213657 +-feature swap of score: 2.67624854996515 instead of -0.349383748322637 +-feature swap of score: 0.524013508116467 instead of -0.214963472143333 +-feature swap of score: 0.611374568656547 instead of -0.415113805180115 +-feature swap of score: -0.0663263752681194 instead of -0.809301260296482 +-feature swap of score: -0.570655323319685 instead of -1.00284058248623 +-feature swap of score: -0.51162567618516 instead of -0.617546456997874 +-feature swap of score: 0.262853014960446 instead of -0.731569312302704 +-feature swap of score: 0.183655849367359 instead of -0.727125998481375 +-feature swap of score: 2.35567914953544 instead of -0.552898637426186 +-feature swap of score: 1.47645384993478 instead of -0.117441427074984 +-feature swap of score: 1.54710472064165 instead of -0.417906335511085 +-feature swap of score: 0.037414679023158 instead of -0.336246268848568 +-feature swap of score: 1.05540893384567 instead of -0.208437609102868 +-feature swap of score: 1.22814783720988 instead of -0.285974745644755 +-feature swap of score: 1.30117098596527 instead of -0.0122657361528397 +-feature swap of score: 1.65041145868476 instead of 0.22215734304035 +-feature swap of score: 0.818318069481163 instead of 0.20494986098483 +-feature swap of score: 0.661806966132295 instead of -0.456947942119838 +-feature swap of score: 3.34181064451229 instead of 0.335859006891459 +-feature swap of score: 2.16022370296709 instead of 0.762629941117762 +-feature swap of score: 2.58327362453296 instead of 0.611508562372541 +-feature swap of score: 0.553543687725917 instead of 0.493696763808768 +-feature swap of score: 2.00226941572817 instead of 0.430915004636696 +-feature swap of score: 4.99658456113679 instead of 0.158213142476702 +-feature swap of score: 1.28524307420142 instead of 0.191090625458121 +-feature swap of score: 5.8781517541959 instead of 0.548488025401874 +-feature swap of score: 2.9490656141014 instead of 0.518960775827558 +-num feature swaps: 59 +* [Sun Jun 29 06:39:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Sat May 25 22:05:38 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 +* [Sun Jun 29 06:40:19 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/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Sat May 25 22:05:50 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 || : +* [Sun Jun 29 06:40:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Sat May 25 22:05:52 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 +* [Sun Jun 29 06:40:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Sat May 25 22:05:54 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 || : +* [Sun Jun 29 06:40:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Sat May 25 22:05:55 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 +* [Sun Jun 29 06:40:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. --number of revised start positions: 11 -* [Sat May 25 22:05:56 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* [Sat May 25 22:05:56 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 +-number of revised start positions: 12 +* [Sun Jun 29 06:40:28 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 29 06:40:28 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/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Sat May 25 22:05:56 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 +* [Sun Jun 29 06:40:28 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/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep -* [Sat May 25 22:05:56 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 +* [Sun Jun 29 06:40:29 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/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.* @@ -13825,12 +13866,14 @@ 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/1081689/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1081689/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/1555680 and its subdirectories -I: Current time: Sat May 25 22:06:26 -12 2024 -I: pbuilder-time-stamp: 1716717986 +I: removing directory /srv/workspace/pbuilder/1081689 and its subdirectories +I: Current time: Sun Jun 29 06:40:45 +14 2025 +I: pbuilder-time-stamp: 1751128845