Diff of the two buildlogs: -- --- b1/build.log 2024-04-23 09:53:14.154060807 +0000 +++ b2/build.log 2024-04-23 10:23:17.741343928 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 26 04:05:43 -12 2025 -I: pbuilder-time-stamp: 1748275543 +I: Current time: Tue Apr 23 23:54:20 +14 2024 +I: pbuilder-time-stamp: 1713866060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,54 +30,86 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/106180/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11624/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 23 09:54 /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/11624/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11624/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='6469ec43155746808c680a235d793283' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='106180' - PS1='# ' - PS2='> ' + INVOCATION_ID=f6e2728b27244535a0d07c0e64234530 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=11624 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.qNNVG8lV/pbuilderrc_BKsP --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.qNNVG8lV/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.qNNVG8lV/pbuilderrc_0zuG --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.qNNVG8lV/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 24 13:36 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/106180/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 23 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/11624/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -280,7 +312,7 @@ Get: 153 http://deb.debian.org/debian unstable/main i386 r-cran-tibble i386 3.2.1+dfsg-2 [421 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] -Fetched 123 MB in 1s (96.5 MB/s) +Fetched 123 MB in 3s (37.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19681 files and directories currently installed.) @@ -799,8 +831,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon May 26 16:06:12 UTC 2025. -Universal Time is now: Mon May 26 16:06:12 UTC 2025. +Local time is now: Tue Apr 23 09:55:46 UTC 2024. +Universal Time is now: Tue Apr 23 09:55:46 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -948,7 +980,11 @@ 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/11624/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/11624/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 @@ -970,7 +1006,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j22 test + make -j10 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' @@ -1012,7 +1048,7 @@ ## 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 -* [Mon May 26 04:06:22 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue Apr 23 23:56:15 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -1064,13 +1100,13 @@ fi -Building a new DB, current time: 05/26/2025 04:06:22 +Building a new DB, current time: 04/23/2024 23:56:16 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 0.00984711 seconds. +Adding sequences from FASTA; added 240 sequences in 0.0244471 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1145,8 +1181,8 @@ 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: 1463.36 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 637.05 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1203,8 +1239,8 @@ 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: 1518.37 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.02 +# Mc/sec: 618.34 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1269,7 +1305,7 @@ 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: 1787.98 +# Mc/sec: 843.92 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1330,7 +1366,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1634.47 +# Mc/sec: 804.87 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1390,8 +1426,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 708.35 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 267.55 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1441,8 +1477,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 542.46 +# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.01 +# Mc/sec: 176.15 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1507,7 +1543,7 @@ 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: 1873.53 +# Mc/sec: 859.17 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1559,8 +1595,8 @@ 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: 00:00:00.00 -# Mc/sec: 632.70 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 227.54 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1611,7 +1647,7 @@ 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: 1681.18 +# Mc/sec: 691.88 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1667,8 +1703,8 @@ 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: 1746.38 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 531.67 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1756,8 +1792,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1292.87 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 443.30 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1841,8 +1877,8 @@ 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: 00:00:00.00 -# Mc/sec: 1602.18 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 568.03 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1898,8 +1934,8 @@ 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: 976.00 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 +# Mc/sec: 331.33 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1955,8 +1991,8 @@ 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: 490.23 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 312.11 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2012,8 +2048,8 @@ 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: 00:00:00.00 -# Mc/sec: 1977.83 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 536.13 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2057,8 +2093,8 @@ 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: 1819.80 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 694.19 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2111,7 +2147,7 @@ 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: 2536.67 +# Mc/sec: 1090.61 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2155,8 +2191,8 @@ 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: 1548.37 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 472.22 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2216,8 +2252,8 @@ 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: 00:00:00.00 -# Mc/sec: 1261.58 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 555.26 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2268,7 +2304,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1274.03 +# Mc/sec: 396.30 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2380,8 +2416,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 1104.18 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 449.24 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2427,8 +2463,8 @@ 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: 00:00:00.00 -# Mc/sec: 1976.68 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 917.24 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2495,7 +2531,7 @@ 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: 1653.77 +# Mc/sec: 750.48 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2534,7 +2570,7 @@ 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: 2801.07 +# Mc/sec: 1459.46 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2610,8 +2646,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1356.28 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 628.28 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2664,7 +2700,7 @@ 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: 1795.67 +# Mc/sec: 858.55 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2748,8 +2784,8 @@ 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: 00:00:00.01 -# Mc/sec: 473.59 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 +# Mc/sec: 185.46 // Query: DLH [M=217] Accession: PF01738.17 @@ -2796,8 +2832,8 @@ 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 0.02s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 2146.68 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1101.54 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2844,7 +2880,7 @@ 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: 1756.69 +# Mc/sec: 738.26 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2894,7 +2930,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1968.38 +# Mc/sec: 1046.84 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2937,7 +2973,7 @@ 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: 2105.94 +# Mc/sec: 1030.26 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -2982,8 +3018,8 @@ 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: 1091.66 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 463.62 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3021,7 +3057,7 @@ 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: 2588.58 +# Mc/sec: 1333.99 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1402.61 +# Mc/sec: 640.83 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3111,7 +3147,7 @@ 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: 1489.73 +# Mc/sec: 689.26 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3149,7 +3185,7 @@ 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: 2455.53 +# Mc/sec: 1339.95 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3199,8 +3235,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1910.35 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 850.92 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3237,8 +3273,8 @@ 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: 00:00:00.00 -# Mc/sec: 2967.29 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1595.79 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3299,7 +3335,7 @@ 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: 1687.00 +# Mc/sec: 808.31 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3344,7 +3380,7 @@ 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: 2027.43 +# Mc/sec: 958.08 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3400,8 +3436,8 @@ 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: 1698.53 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 702.64 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3455,8 +3491,8 @@ 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: 00:00:00.00 -# Mc/sec: 803.08 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 307.23 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3494,7 +3530,7 @@ 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: 2776.60 +# Mc/sec: 1075.42 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3571,7 +3607,7 @@ 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: 1826.70 +# Mc/sec: 721.56 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3635,8 +3671,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 743.96 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 248.33 // Query: FPP [M=866] Accession: PF05911.10 @@ -3686,8 +3722,8 @@ 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: 2022.23 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 +# Mc/sec: 949.07 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3739,8 +3775,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2070.21 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1009.04 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3863,8 +3899,8 @@ 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: 00:00:00.01 -# Mc/sec: 670.46 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 279.35 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3903,7 +3939,7 @@ 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: 1549.44 +# Mc/sec: 704.68 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -3993,8 +4029,8 @@ 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: 840.58 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 333.82 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4044,8 +4080,8 @@ 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: 00:00:00.00 -# Mc/sec: 564.40 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 210.55 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4105,8 +4141,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1431.83 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 650.66 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4211,7 +4247,7 @@ 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: 824.56 +# Mc/sec: 369.87 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4259,7 +4295,7 @@ 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: 2046.48 +# Mc/sec: 970.49 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4333,8 +4369,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1224.29 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 628.57 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4404,8 +4440,8 @@ 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: 00:00:00.00 -# Mc/sec: 1489.71 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 692.54 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4452,8 +4488,8 @@ 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 0.02s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 927.69 +# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02 +# Mc/sec: 334.06 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4523,8 +4559,8 @@ 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: 356.65 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 132.33 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4574,8 +4610,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2555.52 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1261.21 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4626,7 +4662,7 @@ 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: 2253.64 +# Mc/sec: 986.72 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4665,7 +4701,7 @@ 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: 1948.76 +# Mc/sec: 378.67 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4710,7 +4746,7 @@ 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: 1856.65 +# Mc/sec: 900.45 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -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: 1425.84 +# Mc/sec: 646.06 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4844,8 +4880,8 @@ 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: 00:00:00.00 -# Mc/sec: 1059.65 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 479.70 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4945,8 +4981,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 899.76 +# CPU time: 0.06u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 +# Mc/sec: 312.12 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5000,8 +5036,8 @@ 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: 00:00:00.00 -# Mc/sec: 1321.82 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 539.39 // Query: IBR [M=62] Accession: PF01485.20 @@ -5039,7 +5075,7 @@ 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: 1754.34 +# Mc/sec: 599.48 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5086,8 +5122,8 @@ 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: 664.83 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 420.91 // Query: malic [M=182] Accession: PF00390.18 @@ -5126,7 +5162,7 @@ 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: 3046.96 +# Mc/sec: 1443.16 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5163,8 +5199,8 @@ 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: 00:00:00.00 -# Mc/sec: 1173.04 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 497.55 // Query: MatE [M=161] Accession: PF01554.17 @@ -5248,8 +5284,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1222.50 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 287.89 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5286,8 +5322,8 @@ 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: 2701.19 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1287.92 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5461,8 +5497,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 -# Mc/sec: 267.82 +# CPU time: 0.12u 0.00s 00:00:00.11 Elapsed: 00:00:00.11 +# Mc/sec: 94.07 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5504,8 +5540,8 @@ 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: 00:00:00.00 -# Mc/sec: 2181.08 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 614.07 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5561,8 +5597,8 @@ 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: 804.24 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 496.65 // Query: MIP [M=227] Accession: PF00230.19 @@ -5612,8 +5648,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1813.78 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 915.14 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5666,7 +5702,7 @@ 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: 1402.51 +# Mc/sec: 669.75 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5756,8 +5792,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1696.67 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 692.59 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5794,8 +5830,8 @@ 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: 1782.88 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 879.92 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5833,7 +5869,7 @@ 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: 2339.29 +# Mc/sec: 1270.63 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5886,7 +5922,7 @@ 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: 2133.46 +# Mc/sec: 1015.01 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5924,7 +5960,7 @@ 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: 2840.31 +# Mc/sec: 1498.26 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6044,8 +6080,8 @@ 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: 00:00:00.00 -# Mc/sec: 1101.62 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 440.23 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6095,8 +6131,8 @@ 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: 1925.98 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 918.29 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6166,8 +6202,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1658.65 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 741.70 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6219,8 +6255,8 @@ 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: 665.09 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 +# Mc/sec: 428.45 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6282,8 +6318,8 @@ 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 0.02s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1542.29 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 665.92 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6385,8 +6421,8 @@ 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: 298.41 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 112.36 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6433,8 +6469,8 @@ 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: 1996.67 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 903.37 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6485,7 +6521,7 @@ 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: 1378.94 +# Mc/sec: 625.04 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6536,7 +6572,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1892.25 +# Mc/sec: 850.92 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6586,8 +6622,8 @@ 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: 00:00:00.00 -# Mc/sec: 2098.24 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 999.47 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6632,7 +6668,7 @@ 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: 2193.13 +# Mc/sec: 1035.80 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6679,7 +6715,7 @@ 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: 1357.98 +# Mc/sec: 490.72 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6743,8 +6779,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 514.37 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 201.03 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6789,7 +6825,7 @@ 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: 1698.95 +# Mc/sec: 810.02 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6841,8 +6877,8 @@ 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: 656.72 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 358.87 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6886,8 +6922,8 @@ 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: 00:00:00.00 -# Mc/sec: 2271.69 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 829.53 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -6987,8 +7023,8 @@ 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: 544.66 +# CPU time: 0.06u 0.00s 00:00:00.05 Elapsed: 00:00:00.06 +# Mc/sec: 207.71 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7033,7 +7069,7 @@ 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: 746.95 +# Mc/sec: 272.16 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7085,8 +7121,8 @@ 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: 2135.57 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 960.44 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7159,8 +7195,8 @@ 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: 00:00:00.01 -# Mc/sec: 401.59 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 +# Mc/sec: 154.08 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7220,8 +7256,8 @@ 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: 1801.35 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 409.61 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7265,8 +7301,8 @@ 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: 1915.73 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 371.48 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7318,8 +7354,8 @@ 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: 1829.48 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 473.40 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7356,8 +7392,8 @@ 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: 00:00:00.00 -# Mc/sec: 3681.45 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1837.61 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7400,7 +7436,7 @@ 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: 2133.80 +# Mc/sec: 1101.16 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7462,8 +7498,8 @@ 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: 722.13 +# CPU time: 0.06u 0.00s 00:00:00.05 Elapsed: 00:00:00.06 +# Mc/sec: 308.36 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7500,8 +7536,8 @@ 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: 2623.15 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1447.11 // Query: Usher [M=551] Accession: PF00577.19 @@ -7545,8 +7581,8 @@ 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: 2584.23 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1187.82 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7593,7 +7629,7 @@ 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: 855.17 +# Mc/sec: 387.01 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7638,7 +7674,7 @@ 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: 803.13 +# Mc/sec: 272.26 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7683,7 +7719,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 867.02 +# Mc/sec: 343.22 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7738,7 +7774,7 @@ 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: 997.97 +# Mc/sec: 470.44 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7777,7 +7813,7 @@ 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: 509.90 +# Mc/sec: 233.54 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7829,7 +7865,7 @@ 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: 871.52 +# Mc/sec: 466.29 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7877,7 +7913,7 @@ 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: 1405.61 +# Mc/sec: 541.99 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7916,14 +7952,14 @@ 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: 1233.68 +# Mc/sec: 539.24 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Mon May 26 04:06:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon May 26 04:06:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue Apr 23 23:56:20 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/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Tue Apr 23 23:56:20 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: CUFF.60.1.p1, not unique enough -skipping training candidate: CUFF.26.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p3, not unique enough @@ -7950,39 +7986,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Mon May 26 04:06:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Apr 23 23:56:20 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/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 -* [Mon May 26 04:06:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon May 26 04:06:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon May 26 04:06:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Apr 23 23:56:20 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/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Tue Apr 23 23:56:21 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Tue Apr 23 23:56:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Mon May 26 04:06:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon May 26 04:06:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon May 26 04:06:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Apr 23 23:56:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Tue Apr 23 23:56:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Tue Apr 23 23:56:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon May 26 04:06:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Apr 23 23:57:35 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Mon May 26 04:06:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Apr 23 23:57:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon May 26 04:06:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Apr 23 23:57:55 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon May 26 04:06:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Apr 23 23:57:58 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:06:57 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.-.pwm || : +* [Tue Apr 23 23:57:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:06:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Apr 23 23:58:01 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 -feature swap of score: 1.94858034627835 instead of -0.884029553505083 @@ -7992,33 +8028,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Mon May 26 04:06:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Apr 23 23:58:01 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon May 26 04:07:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Apr 23 23:59:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Mon May 26 04:07:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Apr 23 23:59:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon May 26 04:07:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Apr 23 23:59:44 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon May 26 04:07:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Apr 23 23:59:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:07:28 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/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Apr 23 23:59:49 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 1 -* [Mon May 26 04:07:28 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Mon May 26 04:07:28 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/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed +* [Tue Apr 23 23:59:50 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Tue Apr 23 23:59:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Mon May 26 04:07:28 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/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep +* [Tue Apr 23 23:59:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Mon May 26 04:07:28 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/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds +* [Tue Apr 23 23:59:51 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* @@ -8110,7 +8146,7 @@ ../../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 -* [Mon May 26 04:07:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat +* [Tue Apr 23 23:59:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -8134,8 +8170,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Mon May 26 04:07:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon May 26 04:07:32 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 +* [Wed Apr 24 00:00:00 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/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 +* [Wed Apr 24 00:00:01 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough @@ -8810,37 +8846,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Mon May 26 04:07:32 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 +* [Wed Apr 24 00:00:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 -* [Mon May 26 04:07:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores -* [Mon May 26 04:07:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon May 26 04:07:41 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 +* [Wed Apr 24 00:00:02 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 +* [Wed Apr 24 00:00:08 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 +* [Wed Apr 24 00:00:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Mon May 26 04:07:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon May 26 04:07:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon May 26 04:07:41 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 +* [Wed Apr 24 00:00:39 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* [Wed Apr 24 00:00:39 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 +* [Wed Apr 24 00:00:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Mon May 26 04:08:19 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/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 +* [Wed Apr 24 00:02:55 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Mon May 26 04:08:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Wed Apr 24 00:03:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon May 26 04:08:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed Apr 24 00:03:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon May 26 04:08:30 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 || : +* [Wed Apr 24 00:03:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:08:30 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 || : +* [Wed Apr 24 00:03:44 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:08:31 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 +* [Wed Apr 24 00:03:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 @@ -8899,33 +8935,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Mon May 26 04:08:31 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 +* [Wed Apr 24 00:03:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon May 26 04:09:07 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 +* [Wed Apr 24 00:06:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Mon May 26 04:09:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed Apr 24 00:06:49 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon May 26 04:09:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed Apr 24 00:06:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon May 26 04:09:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed Apr 24 00:06:57 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:09:18 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 +* [Wed Apr 24 00:07:01 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 83 -* [Mon May 26 04:09:18 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Mon May 26 04:09:18 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 +* [Wed Apr 24 00:07:02 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* [Wed Apr 24 00:07:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Mon May 26 04:09:18 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 +* [Wed Apr 24 00:07:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Mon May 26 04:09:19 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 +* [Wed Apr 24 00:07:04 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* @@ -8982,8 +9018,8 @@ CDS coords: 80, 427 -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). --Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. --Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. +-Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. +-Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 112, 447 @@ -9018,7 +9054,7 @@ 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 -* [Mon May 26 04:09:20 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 +* [Wed Apr 24 00:07:08 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -9038,8 +9074,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Mon May 26 04:09:22 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon May 26 04:09:23 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 +* [Wed Apr 24 00:07:15 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 +* [Wed Apr 24 00:07:15 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -9077,37 +9113,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Mon May 26 04:09:23 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 +* [Wed Apr 24 00:07:18 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 -* [Mon May 26 04:09:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores -* [Mon May 26 04:09:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon May 26 04:09:33 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/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 +* [Wed Apr 24 00:07:18 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 +* [Wed Apr 24 00:07:27 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/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 +* [Wed Apr 24 00:08:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Mon May 26 04:09:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon May 26 04:09:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon May 26 04:09:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:08:03 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* [Wed Apr 24 00:08:03 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 +* [Wed Apr 24 00:08:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Mon May 26 04:10:11 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 +* [Wed Apr 24 00:10:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Mon May 26 04:10:19 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 || : +* [Wed Apr 24 00:10:28 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon May 26 04:10:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed Apr 24 00:10:31 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon May 26 04:10:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed Apr 24 00:10:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:10:22 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed Apr 24 00:10:35 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:10:23 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/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 +* [Wed Apr 24 00:10:37 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 @@ -9213,33 +9249,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Mon May 26 04:10:23 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/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 +* [Wed Apr 24 00:10:39 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon May 26 04:11:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:12:29 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Mon May 26 04:11:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed Apr 24 00:12:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon May 26 04:11:08 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed Apr 24 00:12:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon May 26 04:11:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed Apr 24 00:12:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:11:10 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 +* [Wed Apr 24 00:12:51 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 43 -* [Mon May 26 04:11:11 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Mon May 26 04:11:11 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed +* [Wed Apr 24 00:12:52 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* [Wed Apr 24 00:12:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Mon May 26 04:11:11 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 +* [Wed Apr 24 00:12:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Mon May 26 04:11:11 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 +* [Wed Apr 24 00:12:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* @@ -9256,32 +9292,32 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', - 'orient' => '-', - 'gene_id' => '', - 'trans_id' => '', 'coords' => [ [ '1642973', '1644586' ] ], + 'trans_id' => '', + 'gene_id' => '', + 'orient' => '-', + 'contig' => 'III', 'asmbl' => 'comp1051_c1_seq1' }; - strand: + - gene_length: 1616 - gene_type: protein-coding - is_pseudogene: 0 mid_pt: 808 - is_5prime_partial: 0 - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + num_exons: 1 source: transdecoder - Model_feat_name: comp1051_c1_seq1.p1 classification: annotated_genes + is_3prime_partial: 0 + is_5prime_partial: 0 + Model_feat_name: comp1051_c1_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding com_name: ORF type:5prime_partial (+),score=83.26 + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + strand: + + gene_length: 1616 asmbl_id: comp1051_c1_seq1 - num_exons: 1 - is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9299,9 +9335,6 @@ Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', - 'gene_id' => '', - 'orient' => '-', - 'contig' => 'I', 'coords' => [ [ 5095548, @@ -9312,22 +9345,25 @@ '5095301' ] ], - 'asmbl' => 'comp1058_c0_seq1' + 'asmbl' => 'comp1058_c0_seq1', + 'contig' => 'I', + 'orient' => '-', + 'gene_id' => '' }; - strand: + - gene_length: 496 - gene_type: protein-coding - is_pseudogene: 0 - mid_pt: 248 - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 source: transdecoder - Model_feat_name: comp1058_c0_seq1.p1 + classification: annotated_genes + is_3prime_partial: 0 is_5prime_partial: 0 + mid_pt: 248 num_exons: 1 - is_3prime_partial: 0 - classification: annotated_genes - com_name: ORF type:5prime_partial (+),score=32.57 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + strand: + + gene_length: 496 asmbl_id: comp1058_c0_seq1 + Model_feat_name: comp1058_c0_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding + com_name: ORF type:5prime_partial (+),score=32.57 gene_synonyms: mRNA_coords CDS_coords @@ -9350,11 +9386,6 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'contig' => 'III', - 'gene_id' => '', - 'orient' => '-', - 'asmbl' => 'comp1112_c0_seq1', 'coords' => [ [ 2380416, @@ -9364,22 +9395,27 @@ 2379717, '2380336' ] - ] + ], + 'trans_id' => '', + 'gene_id' => '', + 'orient' => '-', + 'contig' => 'III', + 'asmbl' => 'comp1112_c0_seq1' }; - gene_type: protein-coding - gene_length: 2081 - strand: + - is_pseudogene: 0 mid_pt: 1041 - is_5prime_partial: 0 + num_exons: 1 + classification: annotated_genes + is_3prime_partial: 0 source: transdecoder - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + is_5prime_partial: 0 + gene_type: protein-coding Model_feat_name: comp1112_c0_seq1.p1 - asmbl_id: comp1112_c0_seq1 + is_pseudogene: 0 com_name: ORF type:complete (+),score=155.28 - classification: annotated_genes - is_3prime_partial: 0 - num_exons: 1 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + gene_length: 2081 + asmbl_id: comp1112_c0_seq1 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9401,9 +9437,6 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'orient' => '-', - 'contig' => 'II', 'trans_id' => '', 'coords' => [ [ @@ -9423,22 +9456,25 @@ '401683' ] ], - 'asmbl' => 'comp1198_c0_seq1' + 'asmbl' => 'comp1198_c0_seq1', + 'contig' => 'II', + 'orient' => '-', + 'gene_id' => '' }; + num_exons: 1 + mid_pt: 299 is_5prime_partial: 0 - Model_feat_name: comp1198_c0_seq1.p1 + is_3prime_partial: 0 + classification: annotated_genes source: transdecoder - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - asmbl_id: comp1198_c0_seq1 com_name: ORF type:internal (+),score=37.56 - classification: annotated_genes - is_3prime_partial: 0 - num_exons: 1 gene_type: protein-coding + is_pseudogene: 0 + Model_feat_name: comp1198_c0_seq1.p1 + asmbl_id: comp1198_c0_seq1 gene_length: 597 strand: + - mid_pt: 299 - is_pseudogene: 0 + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9466,6 +9502,7 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', 'coords' => [ [ 368840, @@ -9477,25 +9514,24 @@ ] ], 'asmbl' => 'comp1210_c0_seq1', - 'gene_id' => '', - 'orient' => '-', 'contig' => 'III', - 'trans_id' => '' + 'orient' => '-', + 'gene_id' => '' }; - com_name: ORF type:5prime_partial (+),score=12.16 asmbl_id: comp1210_c0_seq1 - classification: annotated_genes - is_3prime_partial: 0 - num_exons: 1 - is_5prime_partial: 0 - source: transdecoder + gene_length: 1554 + strand: + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=12.16 + gene_type: protein-coding Model_feat_name: comp1210_c0_seq1.p1 is_pseudogene: 0 + is_5prime_partial: 0 + is_3prime_partial: 0 + classification: annotated_genes + source: transdecoder + num_exons: 1 mid_pt: 777 - gene_type: protein-coding - gene_length: 1554 - strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9520,11 +9556,11 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'asmbl' => 'comp366_c0_seq1', + 'contig' => 'II', 'orient' => '-', 'gene_id' => '', - 'contig' => 'II', - 'asmbl' => 'comp366_c0_seq1', + 'trans_id' => '', 'coords' => [ [ '3840968', @@ -9532,19 +9568,19 @@ ] ] }; + num_exons: 1 mid_pt: 170 - is_pseudogene: 0 - gene_length: 340 - gene_type: protein-coding - strand: - - asmbl_id: comp366_c0_seq1 - com_name: ORF type:internal (-),score=12.83 + is_5prime_partial: 0 classification: annotated_genes - num_exons: 1 is_3prime_partial: 0 - is_5prime_partial: 0 - Model_feat_name: comp366_c0_seq1.p1 source: transdecoder + com_name: ORF type:internal (-),score=12.83 + gene_type: protein-coding + Model_feat_name: comp366_c0_seq1.p1 + is_pseudogene: 0 + gene_length: 340 + asmbl_id: comp366_c0_seq1 + strand: - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 gene_synonyms: mRNA_coords @@ -9571,31 +9607,31 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'gene_id' => '', 'contig' => 'I', 'orient' => '-', - 'gene_id' => '', 'asmbl' => 'comp610_c0_seq1', 'coords' => [ [ '5471264', '5472770' ] - ] + ], + 'trans_id' => '' }; + strand: + + asmbl_id: comp610_c0_seq1 + gene_length: 1509 TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - source: transdecoder + com_name: ORF type:5prime_partial (+),score=50.55 Model_feat_name: comp610_c0_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding is_5prime_partial: 0 + source: transdecoder is_3prime_partial: 0 - num_exons: 1 classification: annotated_genes - asmbl_id: comp610_c0_seq1 - com_name: ORF type:5prime_partial (+),score=50.55 - strand: + - gene_type: protein-coding - gene_length: 1509 - is_pseudogene: 0 + num_exons: 1 mid_pt: 755 gene_synonyms: mRNA_coords @@ -9621,26 +9657,26 @@ '4336727' ] ], - 'asmbl' => 'comp645_c0_seq1', 'trans_id' => '', 'gene_id' => '', + 'asmbl' => 'comp645_c0_seq1', 'orient' => '-', 'contig' => 'I' }; - classification: annotated_genes com_name: ORF type:5prime_partial (+),score=273.35 + gene_type: protein-coding + Model_feat_name: comp645_c0_seq1.p1 + is_pseudogene: 0 + gene_length: 3653 asmbl_id: comp645_c0_seq1 - is_3prime_partial: 0 + strand: + + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 num_exons: 1 + mid_pt: 1827 is_5prime_partial: 0 - Model_feat_name: comp645_c0_seq1.p1 - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + classification: annotated_genes + is_3prime_partial: 0 source: transdecoder - mid_pt: 1827 - is_pseudogene: 0 - strand: + - gene_type: protein-coding - gene_length: 3653 gene_synonyms: mRNA_coords CDS_coords @@ -9666,26 +9702,26 @@ '381243' ] ], - 'asmbl' => 'comp688_c0_seq1', - 'contig' => 'II', + 'trans_id' => '', 'gene_id' => '', + 'asmbl' => 'comp688_c0_seq1', 'orient' => '+', - 'trans_id' => '' + 'contig' => 'II' }; - gene_length: 2784 - gene_type: protein-coding - strand: + - mid_pt: 1392 - is_pseudogene: 0 - Model_feat_name: comp688_c0_seq1.p1 source: transdecoder - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + classification: annotated_genes + is_3prime_partial: 0 is_5prime_partial: 0 + mid_pt: 1392 num_exons: 1 - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=172.54 + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + strand: + + gene_length: 2784 asmbl_id: comp688_c0_seq1 - classification: annotated_genes + Model_feat_name: comp688_c0_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding + com_name: ORF type:complete (+),score=172.54 gene_synonyms: mRNA_coords CDS_coords @@ -9709,6 +9745,9 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'orient' => '+', + 'contig' => 'II', 'asmbl' => 'comp856_c0_seq1', 'coords' => [ [ @@ -9720,25 +9759,22 @@ '3755057' ] ], - 'gene_id' => '', - 'orient' => '+', - 'contig' => 'II', 'trans_id' => '' }; + num_exons: 1 + mid_pt: 785 is_5prime_partial: 0 - source: transdecoder - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 - Model_feat_name: comp856_c0_seq1.p1 - asmbl_id: comp856_c0_seq1 - com_name: ORF type:complete (+),score=71.94 classification: annotated_genes is_3prime_partial: 0 - num_exons: 1 + source: transdecoder + com_name: ORF type:complete (+),score=71.94 gene_type: protein-coding + is_pseudogene: 0 + Model_feat_name: comp856_c0_seq1.p1 gene_length: 1569 + asmbl_id: comp856_c0_seq1 strand: + - is_pseudogene: 0 - mid_pt: 785 + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9758,10 +9794,11 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'gene_id' => '', 'orient' => '-', 'contig' => 'II', + 'asmbl' => 'comp873_c0_seq2', + 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 3727877, @@ -9775,23 +9812,22 @@ 3726988, '3727657' ] - ], - 'asmbl' => 'comp873_c0_seq2' + ] }; - mid_pt: 513 is_pseudogene: 0 - strand: + - gene_length: 1025 + Model_feat_name: comp873_c0_seq2.p1 gene_type: protein-coding - classification: annotated_genes com_name: ORF type:5prime_partial (+),score=8.59 + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + strand: + asmbl_id: comp873_c0_seq2 + gene_length: 1025 + mid_pt: 513 num_exons: 1 + source: transdecoder is_3prime_partial: 0 + classification: annotated_genes is_5prime_partial: 0 - Model_feat_name: comp873_c0_seq2.p1 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 - source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9815,10 +9851,10 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'gene_id' => '', + 'asmbl' => 'comp888_c0_seq1', 'contig' => 'III', 'orient' => '-', - 'gene_id' => '', 'coords' => [ [ 1268244, @@ -9829,22 +9865,22 @@ '1268172' ] ], - 'asmbl' => 'comp888_c0_seq1' + 'trans_id' => '' }; + is_5prime_partial: 0 + classification: annotated_genes is_3prime_partial: 0 + source: transdecoder num_exons: 1 - classification: annotated_genes + mid_pt: 295 + gene_length: 589 asmbl_id: comp888_c0_seq1 - com_name: ORF type:5prime_partial (+),score=23.94 + strand: + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 - source: transdecoder + com_name: ORF type:5prime_partial (+),score=23.94 + gene_type: protein-coding Model_feat_name: comp888_c0_seq1.p1 - is_5prime_partial: 0 is_pseudogene: 0 - mid_pt: 295 - strand: + - gene_type: protein-coding - gene_length: 589 gene_synonyms: mRNA_coords CDS_coords @@ -9866,10 +9902,10 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', 'gene_id' => '', + 'asmbl' => 'comp940_c0_seq1', + 'contig' => 'III', 'orient' => '+', - 'trans_id' => '', 'coords' => [ [ 105641, @@ -9880,22 +9916,22 @@ '106404' ] ], - 'asmbl' => 'comp940_c0_seq1' + 'trans_id' => '' }; TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 - source: transdecoder - Model_feat_name: comp940_c0_seq1.p1 - is_5prime_partial: 0 - is_3prime_partial: 0 - num_exons: 1 - classification: annotated_genes asmbl_id: comp940_c0_seq1 - com_name: ORF type:complete (+),score=94.37 + gene_length: 2129 strand: + gene_type: protein-coding - gene_length: 2129 + Model_feat_name: comp940_c0_seq1.p1 is_pseudogene: 0 + com_name: ORF type:complete (+),score=94.37 + is_3prime_partial: 0 + classification: annotated_genes + source: transdecoder + is_5prime_partial: 0 mid_pt: 1065 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9916,10 +9952,6 @@ Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', - 'contig' => 'I', - 'orient' => '-', - 'gene_id' => '', - 'asmbl' => 'comp983_c0_seq1', 'coords' => [ [ 4100066, @@ -9929,22 +9961,26 @@ 4098246, '4100014' ] - ] + ], + 'contig' => 'I', + 'orient' => '-', + 'asmbl' => 'comp983_c0_seq1', + 'gene_id' => '' }; - gene_length: 1870 - gene_type: protein-coding - strand: + - mid_pt: 935 - is_pseudogene: 0 - Model_feat_name: comp983_c0_seq1.p1 source: transdecoder - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + classification: annotated_genes + is_3prime_partial: 0 is_5prime_partial: 0 + mid_pt: 935 num_exons: 1 - is_3prime_partial: 0 + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + strand: + + gene_length: 1870 asmbl_id: comp983_c0_seq1 + Model_feat_name: comp983_c0_seq1.p1 + is_pseudogene: 0 + gene_type: protein-coding com_name: ORF type:5prime_partial (+),score=143.65 - classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9988,7 +10024,7 @@ ## 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 -* [Mon May 26 04:11:13 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 +* [Wed Apr 24 00:12:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -10013,8 +10049,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Mon May 26 04:11:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon May 26 04:11:30 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 +* [Wed Apr 24 00:13:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:13:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: NM_198270.p1, not unique enough -skipping training candidate: NR_104391.p1, not unique enough -skipping training candidate: NR_104395.p1, not unique enough @@ -12632,37 +12668,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Mon May 26 04:11:32 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 +* [Wed Apr 24 00:13:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Mon May 26 04:11:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon May 26 04:11:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Apr 22 21:49:17 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 +* [Wed Apr 24 00:13:38 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 +* [Wed Apr 24 00:13:47 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 +* [Wed Apr 24 00:15:13 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Mon Apr 22 21:49:18 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* [Mon Apr 22 21:49:18 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 -* [Mon Apr 22 21:49:20 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 +* [Wed Apr 24 00:15:14 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* [Wed Apr 24 00:15:15 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 +* [Wed Apr 24 00:15:18 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon Apr 22 21:49:56 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:16:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Mon Apr 22 21:50:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Wed Apr 24 00:16:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon Apr 22 21:50:07 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 +* [Wed Apr 24 00:17:01 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Apr 22 21:50:08 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed Apr 24 00:17:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon Apr 22 21:50:08 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed Apr 24 00:17:04 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon Apr 22 21:50:09 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 +* [Wed Apr 24 00:17:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 336 num_incorporate: 100 -feature swap of score: 3.78911079353454 instead of -4.15762669956 -feature swap of score: 4.3075564869904 instead of -3.54241712691985 @@ -12765,33 +12801,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Mon Apr 22 21:50:10 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 +* [Wed Apr 24 00:17:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Mon Apr 22 21:50:45 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 +* [Wed Apr 24 00:18:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Mon May 26 04:13:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed Apr 24 00:18:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon May 26 04:13:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed Apr 24 00:18:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon May 26 04:13:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed Apr 24 00:18:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:13:56 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 +* [Wed Apr 24 00:18:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 -* [Mon May 26 04:13:58 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Mon May 26 04:13:58 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/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 +* [Wed Apr 24 00:18:47 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* [Wed Apr 24 00:18:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Mon May 26 04:13:58 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/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 +* [Wed Apr 24 00:18:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Mon May 26 04:14:00 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 +* [Wed Apr 24 00:18:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* @@ -12903,7 +12939,7 @@ // 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 -* [Mon May 26 04:14:10 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 +* [Wed Apr 24 00:19:09 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -12927,14 +12963,14 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Mon May 26 04:14:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon May 26 04:14:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr --skipping training candidate: bdg_i3.p1, not unique enough +* [Wed Apr 24 00:19:13 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 +* [Wed Apr 24 00:19:13 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +-skipping training candidate: bdg_i2.p1, not unique enough -skipping training candidate: bdg_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_i3.p1, not unique enough +-skipping training candidate: eIF5B_i2.p1, not unique enough -skipping training candidate: eIF5B_i4.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough @@ -12945,36 +12981,36 @@ -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i3.p1, not unique enough +-skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough --skipping training candidate: Calx_i4.p1, not unique enough +-skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: Calx_i5.p1, not unique enough -skipping training candidate: Calx_i1.p1, not unique enough --skipping training candidate: Calx_i2.p1, not unique enough +-skipping training candidate: Calx_i4.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough --skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough --skipping training candidate: Klp10A_i1.p1, not unique enough +-skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: Klp10A_i6.p1, not unique enough +-skipping training candidate: Klp10A_i2.p1, not unique enough -skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough --skipping training candidate: Klp10A_i2.p1, not unique enough --skipping training candidate: CG6424_i1.p1, not unique enough --skipping training candidate: CG6424_i4.p1, not unique enough +-skipping training candidate: Klp10A_i1.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough +-skipping training candidate: CG6424_i4.p1, not unique enough +-skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough --skipping training candidate: CG33970_i2.p1, not unique enough +-skipping training candidate: CG33970_i1.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough --skipping training candidate: CG12581_i2.p1, not unique enough --skipping training candidate: CG6091_i1.p1, not unique enough +-skipping training candidate: CG12581_i1.p1, not unique enough +-skipping training candidate: CG6091_i3.p1, not unique enough +-skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: hrg_i2.p1, not unique enough -skipping training candidate: hrg_i3.p1, not unique enough --skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p1, not unique enough @@ -12983,169 +13019,169 @@ -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough -skipping training candidate: l(3)05822_i3.p1, not unique enough --skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i4.p1, not unique enough +-skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough -skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough --skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough --skipping training candidate: Hsc70-1_i2.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: Est-6_i1.p1, not unique enough +-skipping training candidate: Hsc70-1_i2.p1, not unique enough +-skipping training candidate: Est-6_i2.p1, not unique enough -skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: S-Lap3_i3.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_i2.p1, not unique enough --skipping training candidate: CG30438_i3.p1, not unique enough +-skipping training candidate: CG30438_i1.p1, not unique enough -skipping training candidate: CG30438_i5.p1, not unique enough +-skipping training candidate: CG30438_i2.p1, not unique enough -skipping training candidate: CG6145_i4.p1, not unique enough -skipping training candidate: CG33970_i3.p1, not unique enough -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough --skipping training candidate: Eno_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_i3.p1, not unique enough +-skipping training candidate: Eno_i5.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_i6.p1, not unique enough -skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_i7.p1, not unique enough +-skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_i3.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_i3.p1, not unique enough +-skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough --skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i1.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: CG6424_i4.p2, not unique enough --skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: Eno_i3.p2, not unique enough +-skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: CG6424_i3.p2, not unique enough +-skipping training candidate: CG6424_i4.p2, not unique enough +-skipping training candidate: CG6424_i1.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough --skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Irk2_i4.p1, not unique enough +-skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i3.p1, not unique enough --skipping training candidate: AdipoR_i4.p1, not unique enough -skipping training candidate: AdipoR_i2.p1, not unique enough --skipping training candidate: Tm1_i5.p1, not unique enough +-skipping training candidate: AdipoR_i4.p1, not unique enough +-skipping training candidate: AdipoR_i5.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough +-skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough --skipping training candidate: kto_i1.p2, not unique enough +-skipping training candidate: kto_i2.p3, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough --skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i1.p1, not unique enough -skipping training candidate: nmo_i7.p1, not unique enough --skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: CG8136_i1.p1, not unique enough +-skipping training candidate: CG8136_i3.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough -skipping training candidate: CG7564_i2.p3, not unique enough --skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG7564_i1.p1, not unique enough +-skipping training candidate: 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 -skipping training candidate: nmo_i5.p1, not unique enough +-skipping training candidate: nmo_i2.p1, not unique enough +-skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough --skipping training candidate: CG6024_i1.p1, not unique enough +-skipping training candidate: CG6024_i2.p1, not unique enough -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough +-skipping training candidate: ogre_i4.p1, not unique enough +-skipping training candidate: ogre_i6.p1, not unique enough -skipping training candidate: ogre_i1.p1, not unique enough -skipping training candidate: ogre_i5.p1, not unique enough --skipping training candidate: ogre_i4.p1, not unique enough -skipping training candidate: ogre_i2.p1, not unique enough --skipping training candidate: ogre_i6.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough -skipping training candidate: Gale_i2.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough -skipping training candidate: CG13284_i3.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough --skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: CG13284_i2.p1, not unique enough +-skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough --skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Klp10A_i6.p2, not unique enough +-skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Klp10A_i3.p2, not unique enough -skipping training candidate: Klp10A_i4.p2, not unique enough --skipping training candidate: Klp10A_i2.p2, not unique enough +-skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: sqd_i2.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_i1.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: l(3)05822_i2.p2, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough -skipping training candidate: l(3)05822_i3.p2, not unique enough --skipping training candidate: Tm1_i6.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_i3.p1, not unique enough +-skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough --skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Npl4_i1.p2, not unique enough +-skipping training candidate: Tm1_i3.p1, 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_i2.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough --skipping training candidate: CG8312_i2.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough --skipping training candidate: Dgk_i7.p2, not unique enough --skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: CG8312_i2.p2, not unique enough +-skipping training candidate: Dgk_i1.p2, not unique enough +-skipping training candidate: eIF5B_i1.p2, not unique enough -skipping training candidate: eIF5B_i3.p2, not unique enough +-skipping training candidate: eIF5B_i2.p2, not unique enough -skipping training candidate: eIF5B_i4.p2, not unique enough --skipping training candidate: eIF5B_i1.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: Dgk_i3.p2, not unique enough --skipping training candidate: l(1)G0193_i2.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: Dgk_i1.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_i6.p3, not unique enough --skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: Dgk_i2.p3, not unique enough -skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough -skipping training candidate: l(3)05822_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough --skipping training candidate: CG6024_i1.p2, not unique enough --skipping training candidate: Sec16_i6.p2, not unique enough +-skipping training candidate: CG6024_i2.p2, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: CG13887_i1.p1, not unique enough +-skipping training candidate: Sec16_i6.p2, not unique enough -skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG14995_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_i6.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough --skipping training candidate: nmo_i2.p2, not unique enough -skipping training candidate: nmo_i5.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_i7.p2, not unique enough +-skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i4.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough @@ -13156,345 +13192,345 @@ -skipping training candidate: gukh_i4.p3, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough +-skipping training candidate: RpL15_i1.p1, not unique enough +-skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough -skipping training candidate: RpL15_i3.p1, not unique enough --skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough --skipping training candidate: RpL15_i1.p1, not unique enough --skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: Npl4_i2.p3, not unique enough +-skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: trc_i1.p2, not unique enough +-skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough --skipping training candidate: Hsc70-1_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough --skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough --skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: CG14995_i2.p2, not unique enough +-skipping training candidate: CG10237_i5.p2, not unique enough -skipping training candidate: CG10237_i2.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, 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: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i3.p3, not unique enough -skipping training candidate: Eno_i4.p3, not unique enough +-skipping training candidate: Eno_i3.p3, not unique enough +-skipping training candidate: Eno_i5.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough -skipping training candidate: CG14995_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: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough +-skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough --skipping training candidate: CG30438_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.p3, not unique enough +-skipping training candidate: CG30438_i1.p2, not unique enough -skipping training candidate: CG30438_i5.p2, not unique enough +-skipping training candidate: CG30438_i2.p2, not unique enough +-skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough --skipping training candidate: cdi_i1.p3, not unique enough +-skipping training candidate: cdi_i2.p2, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough --skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CanB2_i1.p1, not unique enough +-skipping training candidate: CG14995_i2.p3, not unique enough +-skipping training candidate: CanB2_i2.p1, not unique enough -skipping training candidate: ADD1_i2.p2, not unique enough -skipping training candidate: Sec16_i3.p3, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough -skipping training candidate: bic_i2.p1, not unique enough --skipping training candidate: CG12581_i2.p2, not unique enough +-skipping training candidate: CG12581_i1.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i1.p1, not unique enough +-skipping training candidate: ctp_i2.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: hrg_i3.p2, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough --skipping training candidate: Eno_i6.p4, not unique enough +-skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: Eno_i1.p4, not unique enough --skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i3.p4, not unique enough -skipping training candidate: Eno_i4.p4, not unique enough --skipping training candidate: Klp10A_i1.p3, not unique enough +-skipping training candidate: Eno_i3.p4, not unique enough +-skipping training candidate: Eno_i5.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Klp10A_i6.p3, not unique enough +-skipping training candidate: Klp10A_i2.p4, not unique enough -skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough --skipping training candidate: Calx_i4.p2, not unique enough --skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Klp10A_i1.p3, 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_i3.p2, not unique enough --skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i6.p2, not unique enough --skipping training candidate: Calx_i2.p2, not unique enough +-skipping training candidate: Calx_i1.p2, not unique enough +-skipping training candidate: Calx_i3.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough +-skipping training candidate: Calx_i4.p2, not unique enough +-skipping training candidate: Calx_i9.p2, not unique enough +-skipping training candidate: Calx_i8.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_i4.p2, not unique enough --skipping training candidate: CG7564_i4.p3, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough +-skipping training candidate: CG7564_i4.p2, not unique enough +-skipping training candidate: CG7564_i4.p3, not unique enough -skipping training candidate: Gale_i2.p2, not unique enough --skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i1.p3, not unique enough -skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: eIF5B_i2.p3, not unique enough -skipping training candidate: eIF5B_i4.p3, not unique enough --skipping training candidate: eIF5B_i1.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_i4.p3, not unique enough --skipping training candidate: CG6424_i2.p3, not unique enough -skipping training candidate: CG6424_i3.p3, not unique enough --skipping training candidate: CG6424_i3.p4, not unique enough --skipping training candidate: Tm1_i13.p2, not unique enough --skipping training candidate: Tm1_i5.p2, not unique enough +-skipping training candidate: CG6424_i4.p3, not unique enough +-skipping training candidate: CG6424_i1.p3, not unique enough +-skipping training candidate: CG6424_i1.p4, not unique enough -skipping training candidate: Tm1_i14.p2, not unique enough --skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Tm1_i16.p2, not unique enough +-skipping training candidate: Tm1_i5.p2, not unique enough -skipping training candidate: Dgk_i7.p5, not unique enough --skipping training candidate: cdi_i1.p4, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i1.p4, not unique enough +-skipping training candidate: Dgk_i2.p5, not unique enough +-skipping training candidate: cdi_i2.p3, not unique enough -skipping training candidate: eff_i2.p1, not unique enough --skipping training candidate: eff_i3.p1, not unique enough +-skipping training candidate: eff_i1.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i2.p4, not unique enough +-skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i3.p4, not unique enough +-skipping training candidate: eIF5B_i2.p4, not unique enough -skipping training candidate: eIF5B_i4.p5, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough --skipping training candidate: Sec16_i3.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_i6.p3, not unique enough -skipping training candidate: Sec16_i5.p4, not unique enough +-skipping training candidate: Sec16_i6.p3, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: Sec16_i4.p5, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough -skipping training candidate: CG32082_i2.p2, not unique enough -skipping training candidate: CG32082_i3.p2, not unique enough --skipping training candidate: CG3530_i2.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough --skipping training candidate: Dgk_i7.p6, not unique enough +-skipping training candidate: CG3530_i1.p2, not unique enough +-skipping training candidate: Dgk_i2.p6, not unique enough -skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough -skipping training candidate: sqd_i2.p2, not unique enough -skipping training candidate: CG7564_i2.p6, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: CG7564_i1.p4, not unique enough +-skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough --skipping training candidate: cdi_i1.p5, not unique enough +-skipping training candidate: cdi_i2.p4, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough -skipping training candidate: CG6091_i3.p2, not 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enough --skipping training candidate: Aldh-III_i11.p2, not unique enough +-skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: Aldh-III_i8.p2, not unique enough +-skipping training candidate: Aldh-III_i11.p2, not unique enough +-skipping training candidate: CG13284_i2.p2, not unique enough -skipping training candidate: CG13284_i4.p2, not unique enough --skipping training candidate: CG13284_i1.p2, not unique enough +-skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough --skipping training candidate: CG13284_i2.p2, not unique enough +-skipping training candidate: Lip4_i2.p2, not unique enough -skipping training candidate: Lip4_i3.p2, not unique enough --skipping training candidate: Lip4_i1.p2, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough --skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough --skipping training candidate: Dgk_i7.p7, not unique enough --skipping training candidate: Tm1_i13.p3, not unique enough --skipping training candidate: Tm1_i5.p3, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Dgk_i2.p7, not unique enough -skipping training candidate: Tm1_i14.p3, not unique enough --skipping training candidate: CG8312_i2.p3, not unique enough --skipping training candidate: CG8312_i2.p4, not unique enough --skipping training candidate: CG8312_i4.p3, not unique enough --skipping training candidate: CG8312_i4.p4, not unique enough +-skipping training candidate: Tm1_i16.p3, not unique enough +-skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: CG8312_i1.p2, not unique enough -skipping training candidate: CG8312_i1.p3, not unique enough --skipping training candidate: Klp10A_i1.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_i2.p6, not unique enough -skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i4.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i1.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: eff_i1.p2, not unique enough -skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG14995_i5.p5, not unique enough -skipping training candidate: CG14995_i6.p4, not unique enough +-skipping training candidate: CG14995_i5.p5, not unique enough -skipping training candidate: CG14995_i4.p4, not unique enough --skipping training candidate: CG6424_i4.p4, not unique enough --skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i3.p5, not unique enough --skipping training candidate: CG12581_i2.p3, not unique enough +-skipping training candidate: CG6424_i4.p4, not unique enough +-skipping training candidate: CG6424_i1.p5, not unique enough +-skipping training candidate: CG12581_i1.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: CG32082_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: Cnx99A_i3.p3, not unique enough -skipping training candidate: Cdep_i4.p2, not unique enough --skipping training candidate: Cdep_i2.p6, not unique enough +-skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough -skipping training candidate: CG33970_i2.p3, not unique enough --skipping training candidate: CG33970_i3.p3, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough +-skipping training candidate: Sec16_i5.p6, not unique enough +-skipping training candidate: Sec16_i6.p5, not unique enough +-skipping training candidate: Sec16_i3.p6, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough --skipping training candidate: Sec16_i6.p5, not unique enough --skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough --skipping training candidate: CG6024_i1.p4, not unique enough --skipping training candidate: Myo61F_i3.p2, not unique enough +-skipping training candidate: CG6024_i2.p4, not unique enough -skipping training candidate: Myo61F_i2.p2, not unique enough +-skipping training candidate: Myo61F_i1.p2, not unique enough -skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: Cnx99A_i2.p4, not unique enough --skipping training candidate: CG13887_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: CG13887_i4.p2, not unique enough +-skipping training candidate: CG13887_i1.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough --skipping training candidate: CG6145_i2.p2, not unique enough -skipping training candidate: CG6145_i4.p2, not unique enough -skipping training candidate: CG6145_i3.p2, not unique enough --skipping training candidate: Calx_i4.p3, not unique enough --skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough --skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i3.p3, not unique enough --skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i6.p3, not unique enough --skipping training candidate: Calx_i2.p3, not unique enough +-skipping training candidate: Calx_i1.p3, not unique enough +-skipping training candidate: Calx_i3.p3, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough +-skipping training candidate: Calx_i4.p3, not unique enough +-skipping training candidate: Calx_i9.p3, not unique enough +-skipping training candidate: Calx_i8.p3, not unique enough -skipping training candidate: mge_i1.p2, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough --skipping training candidate: AdipoR_i3.p3, not unique enough --skipping training candidate: AdipoR_i4.p3, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough +-skipping training candidate: AdipoR_i1.p2, not unique enough +-skipping training candidate: Aldh-III_i1.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough -skipping training candidate: Aldh-III_i7.p2, not unique enough --skipping training candidate: Aldh-III_i1.p2, not unique enough +-skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i9.p2, not unique enough --skipping training candidate: Cdep_i3.p4, 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_i2.p9, not unique enough +-skipping training candidate: Cdep_i3.p4, not unique enough +-skipping training candidate: Cdep_i1.p4, not unique enough +-skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough -skipping training candidate: hrg_i3.p4, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough --skipping training candidate: CG12581_i2.p4, not unique enough --skipping training candidate: Sec16_i3.p7, not unique enough --skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: CG12581_i1.p4, 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_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_i6.p6, not unique enough +-skipping training candidate: Sec16_i6.p7, not unique enough +-skipping training candidate: Sec16_i3.p7, not unique enough +-skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i4.p8, not unique enough +-skipping training candidate: Sec16_i4.p9, not unique enough -skipping training candidate: 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: CG6091_i1.p4, not unique enough --skipping training candidate: CanB2_i1.p2, not unique enough --skipping training candidate: IP3K1_i2.p2, not unique enough --skipping training candidate: Klp10A_i1.p6, not unique enough +-skipping training candidate: CanB2_i2.p2, 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_i2.p8, not unique enough -skipping training candidate: Klp10A_i3.p5, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough --skipping training candidate: Klp10A_i2.p8, not unique enough +-skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough --skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i4.p4, not unique enough --skipping training candidate: Cdep_i2.p10, not unique enough --skipping training candidate: Est-6_i1.p2, not unique enough --skipping training candidate: Klp10A_i1.p7, not unique enough +-skipping training candidate: Cdep_i3.p5, not unique enough +-skipping training candidate: Cdep_i1.p5, not unique enough +-skipping training candidate: Est-6_i2.p2, not unique enough -skipping training candidate: Klp10A_i6.p6, not unique enough +-skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: Klp10A_i3.p6, not unique enough -skipping training candidate: Klp10A_i4.p6, not unique enough --skipping training candidate: Klp10A_i2.p9, not unique enough +-skipping training candidate: Klp10A_i1.p7, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i3.p5, not unique enough --skipping training candidate: Cnx99A_i4.p3, not unique enough +-skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Cnx99A_i2.p5, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough +-skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough +-skipping training candidate: Myo61F_i1.p3, not unique enough -skipping training candidate: Myo61F_i4.p3, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough +-skipping training candidate: Myo61F_i1.p4, not unique enough -skipping training candidate: Myo61F_i4.p4, not unique enough -skipping training candidate: bic_i2.p2, not unique enough -skipping training candidate: CG10082_i2.p3, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough -skipping training candidate: CG32082_i2.p4, 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: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i3.p5, not unique enough -skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: Eno_i3.p5, not unique enough +-skipping training candidate: Eno_i5.p6, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough -skipping training candidate: Sec16_i4.p10, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough --skipping training candidate: Dgk_i6.p6, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: Dgk_i5.p5, not unique enough --skipping training candidate: Dgk_i7.p8, not unique enough --skipping training candidate: nmo_i6.p3, not unique enough --skipping training candidate: CG33970_i2.p5, not unique enough +-skipping training candidate: Dgk_i1.p6, not unique enough +-skipping training candidate: Dgk_i2.p8, not unique enough +-skipping training candidate: nmo_i4.p3, not unique enough +-skipping training candidate: CG33970_i1.p4, not unique enough -skipping training candidate: sqd_i3.p2, not unique enough --skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: Dgk_i3.p7, not unique enough --skipping training candidate: His4r_i3.p1, not unique enough --skipping training candidate: His4r_i2.p1, not unique enough +-skipping training candidate: Dgk_i1.p7, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough +-skipping training candidate: His4r_i2.p1, not unique enough +-skipping training candidate: His4r_i1.p1, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough --skipping training candidate: Hsc70-1_i3.p4, not unique enough +-skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: hrg_i3.p5, not unique enough --skipping training candidate: hrg_i4.p6, not unique enough --skipping training candidate: CG8136_i4.p2, not unique enough --skipping training candidate: CG8136_i2.p2, not unique enough -skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough +-skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: CG8136_i2.p2, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough +-skipping training candidate: Myo61F_i1.p5, not unique enough -skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: 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: CG6091_i1.p5, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough --skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: gukh_i2.p3, not unique enough -skipping training candidate: sqd_i3.p3, not unique enough -skipping training candidate: CG33125_i1.p4, not unique enough @@ -13502,124 +13538,125 @@ -redundancy-minimized set includes 286 / 856 = 33.41% -* [Mon May 26 04:14:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:19:13 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 49.4 -* [Mon May 26 04:14:12 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon May 26 04:14:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon May 26 04:14:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:19:14 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 +* [Wed Apr 24 00:19:15 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 +* [Wed Apr 24 00:19:29 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Mon May 26 04:14:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon May 26 04:14:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon May 26 04:14:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:19:30 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* [Wed Apr 24 00:19:30 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 +* [Wed Apr 24 00:19:31 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon May 26 04:14:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed Apr 24 00:20:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Mon May 26 04:15:05 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 || : +* [Wed Apr 24 00:21:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon May 26 04:15:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed Apr 24 00:21:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon May 26 04:15:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed Apr 24 00:21:08 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:15:08 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 || : +* [Wed Apr 24 00:21:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:15:09 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 +* [Wed Apr 24 00:21:11 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/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: -1.38551294114858 instead of -3.66616038948466 --feature swap of score: -1.41382719425334 instead of -3.43495288410532 --feature swap of score: -1.68418261971974 instead of -2.91177634727783 --feature swap of score: -1.40705005507333 instead of -1.46617496621787 --feature swap of score: -0.56960165140243 instead of -1.07721164028339 --feature swap of score: 1.99617145955636 instead of -1.03320018474832 --feature swap of score: -0.468245500358358 instead of -0.966907548177056 --feature swap of score: 2.81204536437025 instead of -0.950070420605187 --feature swap of score: -0.557547949398314 instead of -0.988033216212022 --feature swap of score: 2.34934606354628 instead of -0.964282912932188 --feature swap of score: -0.318128401233888 instead of -0.842694050268766 --feature swap of score: 0.612047899322094 instead of -1.0515962264697 --feature swap of score: 1.76550144646207 instead of -1.14181006225225 --feature swap of score: 1.30677700896704 instead of -1.45441151111424 --feature swap of score: -0.679698942005933 instead of -1.01451772520229 --feature swap of score: -0.0527176835745414 instead of -0.921969024820931 --feature swap of score: -0.54360682237528 instead of -1.20722859120651 --feature swap of score: -0.417735061605544 instead of -0.493848877100696 --feature swap of score: 1.34560160932448 instead of -0.471342237461974 --feature swap of score: -1.74065199049715 instead of -1.91542318317964 --feature swap of score: 3.12464846827593 instead of -0.66188401431984 --feature swap of score: 1.88627355013333 instead of -0.520305713084577 --feature swap of score: 0.825401189650838 instead of -0.242900015732982 --feature swap of score: 2.77375438201309 instead of -0.330154941823902 --feature swap of score: 0.357709926165495 instead of -0.326931270520194 --feature swap of score: 2.36062790015408 instead of -0.774260612524082 --feature swap of score: 0.765973158531224 instead of -0.477089317179769 --feature swap of score: 1.42245400122527 instead of -0.442334126921751 --feature swap of score: 0.829951785741269 instead of -0.455979350831954 --feature swap of score: 3.0990022411827 instead of -0.574779302601912 --feature swap of score: 0.100019363394678 instead of -0.648148657762391 --feature swap of score: 0.959621493123935 instead of -0.883704103927076 --feature swap of score: 0.292516100713166 instead of -1.00255853596094 --feature swap of score: 1.39428422981122 instead of -1.29290621649429 --feature swap of score: 0.855042771470122 instead of -0.892710534569608 --feature swap of score: 0.181573749762607 instead of -0.519199312447935 --feature swap of score: 0.0778223348646312 instead of -0.848185812413239 --feature swap of score: 0.322677357946044 instead of -0.649583782158351 --feature swap of score: 0.713681541626403 instead of -0.661783015963336 --feature swap of score: 2.20826402284344 instead of -0.367860217027351 --feature swap of score: 0.257950117483475 instead of -0.145844588624463 --feature swap of score: 0.120956816766602 instead of -0.46421530946553 --feature swap of score: -0.334218044986113 instead of -0.356751579652435 --feature swap of score: 1.11431901968986 instead of -0.49922623565137 --feature swap of score: 1.03662429388729 instead of -0.30676307654871 --feature swap of score: -0.0847409586703537 instead of -0.12849732346074 --feature swap of score: 0.827713554368657 instead of -0.290652312679979 --feature swap of score: 3.40240893832216 instead of 0.295604444138581 --feature swap of score: 0.399225531344102 instead of 0.239312902176572 --feature swap of score: 0.876877899166918 instead of 0.00969472989931586 --feature swap of score: 1.99097342690348 instead of 0.130222736722669 --feature swap of score: 0.784067076884655 instead of 0.279499045725796 --feature swap of score: 0.520263812697764 instead of 0.452477039272881 --feature swap of score: 0.737263930331001 instead of 0.472145654261766 --feature swap of score: 6.81047508445808 instead of 0.343504306636728 --feature swap of score: 1.96394330333605 instead of 0.480382628947226 --feature swap of score: 0.862199516865658 instead of 0.358017369319397 --feature swap of score: 8.52316493598183 instead of -0.286938538868064 --num feature swaps: 58 -* [Mon May 26 04:15:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +-feature swap of score: -1.24309650720845 instead of -3.388219083446 +-feature swap of score: -1.6106174472298 instead of -3.21222145841815 +-feature swap of score: -1.81600207135382 instead of -2.67321105052067 +-feature swap of score: -1.38634949813591 instead of -1.74761768704142 +-feature swap of score: -0.584403911562186 instead of -1.33044382128554 +-feature swap of score: -0.681096564489819 instead of -1.21395157464085 +-feature swap of score: 1.99535900147302 instead of -0.954177006062411 +-feature swap of score: -0.532108105193645 instead of -1.19291409158393 +-feature swap of score: 2.82474680886101 instead of -0.969949969544144 +-feature swap of score: -0.587496250715497 instead of -2.41319698601139 +-feature swap of score: 2.37689459851348 instead of -1.23029034988598 +-feature swap of score: -0.784851580858306 instead of -1.31037998384217 +-feature swap of score: 0.227896105711391 instead of -1.55318988180264 +-feature swap of score: 1.13574051006973 instead of -1.10829322598629 +-feature swap of score: 1.93616923105006 instead of -1.20080972296901 +-feature swap of score: -0.192404653007029 instead of -0.950153945997903 +-feature swap of score: -0.667460389480695 instead of -1.13062602578859 +-feature swap of score: 0.462029712905814 instead of -1.24058378324466 +-feature swap of score: 0.189012253319057 instead of -0.926810161264384 +-feature swap of score: 0.703897700398698 instead of -0.82239298610131 +-feature swap of score: 3.54186604488738 instead of -0.385362730338034 +-feature swap of score: 1.33375639575289 instead of -0.403762237754607 +-feature swap of score: 0.148431890950147 instead of -0.475949033990299 +-feature swap of score: 2.78046350335731 instead of -0.66129987225147 +-feature swap of score: -0.526883121018276 instead of -0.57189247782397 +-feature swap of score: -0.280979411159657 instead of -0.389795179106051 +-feature swap of score: 0.209047272833346 instead of -0.0560153043487653 +-feature swap of score: 1.47473759189045 instead of -0.326511319521421 +-feature swap of score: 1.79540009641093 instead of -0.471078109890551 +-feature swap of score: 0.938967806068656 instead of -0.364652354423762 +-feature swap of score: 0.0828517132273195 instead of -0.400635595272438 +-feature swap of score: 2.87245583400989 instead of -0.509636107904986 +-feature swap of score: -0.505839143176967 instead of -0.712555642991932 +-feature swap of score: 0.848018904870408 instead of -0.692075651343274 +-feature swap of score: 1.3323643940328 instead of -0.723707935866668 +-feature swap of score: 0.395055194891081 instead of -0.77362064051711 +-feature swap of score: 0.0407615111908492 instead of -0.979395763876878 +-feature swap of score: -0.0484125171544465 instead of -0.818479155755344 +-feature swap of score: 0.649519394490609 instead of -0.609949245323685 +-feature swap of score: -0.0598220610968532 instead of -0.928149338292742 +-feature swap of score: 2.91209084991234 instead of -0.54103367077471 +-feature swap of score: 1.26266240422324 instead of -0.206158519801494 +-feature swap of score: 1.714204644897 instead of 0.0804139076946202 +-feature swap of score: 0.625687900717981 instead of 0.0508774378298835 +-feature swap of score: 0.609600395679125 instead of 0.150339175327561 +-feature swap of score: 1.93100594836698 instead of 0.110837634064345 +-feature swap of score: 0.78068042202871 instead of -0.259214563877692 +-feature swap of score: 0.645021258379563 instead of -0.355108445627323 +-feature swap of score: 3.43445439804309 instead of -0.305853521029369 +-feature swap of score: 0.964669848246328 instead of 0.252955298122401 +-feature swap of score: 1.87368463480903 instead of 0.0930260257890961 +-feature swap of score: 1.13010719756983 instead of 0.272208545573469 +-feature swap of score: 0.737267466579684 instead of 0.193425994031488 +-feature swap of score: 1.32963893732965 instead of 0.594099025535915 +-feature swap of score: 7.35672962010767 instead of 0.913525471156312 +-feature swap of score: 0.89168137456999 instead of 0.789870277335614 +-feature swap of score: 0.559722411735971 instead of 0.555622557314023 +-feature swap of score: 8.84272448850712 instead of 0.518558120082821 +-feature swap of score: 1.62528230155901 instead of 0.633757088502423 +-num feature swaps: 59 +* [Wed Apr 24 00:21:11 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/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 -* [Mon May 26 04:15:44 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/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 +* [Wed Apr 24 00:22:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Mon May 26 04:15:52 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 || : +* [Wed Apr 24 00:22:42 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon May 26 04:15:53 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 +* [Wed Apr 24 00:22:44 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon May 26 04:15:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed Apr 24 00:22:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon May 26 04:15:55 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 +* [Wed Apr 24 00:22:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 14 -* [Mon May 26 04:15:55 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Mon May 26 04:15:55 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/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed +* [Wed Apr 24 00:22:48 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* [Wed Apr 24 00:22:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Mon May 26 04:15:55 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/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 +* [Wed Apr 24 00:22:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep -* [Mon May 26 04:15:55 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/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 +* [Wed Apr 24 00:22:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* @@ -13635,9 +13672,9 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. @@ -13777,12 +13814,14 @@ 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/11624/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11624/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/106180 and its subdirectories -I: Current time: Mon May 26 04:16:13 -12 2025 -I: pbuilder-time-stamp: 1748276173 +I: removing directory /srv/workspace/pbuilder/11624 and its subdirectories +I: Current time: Wed Apr 24 00:23:16 +14 2024 +I: pbuilder-time-stamp: 1713867796