Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 10:08:41.082286732 +0000 +++ b2/build.log 2024-05-07 10:32:10.790259219 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 9 04:21:23 -12 2025 -I: pbuilder-time-stamp: 1749486083 +I: Current time: Wed May 8 00:08:44 +14 2024 +I: pbuilder-time-stamp: 1715076524 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1499937/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/975252/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 7 10:09 /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/975252/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/975252/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6494737e739a4cd680122dc64ca18d4b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1499937' - PS1='# ' - PS2='> ' + INVOCATION_ID=f72e83a15c1d487bac05d8cb6472cd88 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=975252 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.vECcvp3D/pbuilderrc_vC2i --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.vECcvp3D/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.vECcvp3D/pbuilderrc_WAuI --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.vECcvp3D/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 9 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1499937/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 7 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/975252/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -277,7 +309,7 @@ Get: 153 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] -Fetched 123 MB in 5s (24.9 MB/s) +Fetched 123 MB in 4s (29.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -796,8 +828,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 9 16:22:21 UTC 2025. -Universal Time is now: Mon Jun 9 16:22:21 UTC 2025. +Local time is now: Tue May 7 10:10:02 UTC 2024. +Universal Time is now: Tue May 7 10:10:02 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -945,7 +977,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes +I: user script /srv/workspace/pbuilder/975252/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/975252/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 @@ -967,7 +1003,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j42 test + make -j20 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' @@ -1009,7 +1045,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Mon Jun 9 04:22:33 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 +* [Wed May 8 00:10:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -1061,13 +1097,13 @@ fi -Building a new DB, current time: 06/09/2025 04:22:34 +Building a new DB, current time: 05/08/2024 00:10:33 New DB name: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/mini_sprot.db.pep New DB title: mini_sprot.db.pep Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B -Adding sequences from FASTA; added 240 sequences in 0.00720787 seconds. +Adding sequences from FASTA; added 240 sequences in 0.056149 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1142,8 +1178,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1550.56 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 854.03 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1200,8 +1236,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1602.91 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 733.39 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1266,7 +1302,7 @@ 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: 2256.78 +# Mc/sec: 1301.06 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1327,7 +1363,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2157.04 +# Mc/sec: 1186.22 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1387,8 +1423,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 818.37 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 332.12 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1438,8 +1474,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 692.43 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 261.86 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1504,7 +1540,7 @@ 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: 2394.20 +# Mc/sec: 1338.40 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1556,8 +1592,8 @@ 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: 774.08 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 250.83 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1607,8 +1643,8 @@ 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: 2261.93 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.06 +# Mc/sec: 35.80 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1665,7 +1701,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2282.10 +# Mc/sec: 961.95 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1753,8 +1789,8 @@ 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: 1777.65 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 794.81 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1838,8 +1874,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2009.91 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 782.45 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1895,8 +1931,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1067.45 +# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 428.82 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1952,8 +1988,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1190.20 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 397.40 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2010,7 +2046,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 3030.01 +# Mc/sec: 1282.19 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2054,8 +2090,8 @@ 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: 2491.29 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1458.59 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2108,7 +2144,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3025.95 +# Mc/sec: 1885.09 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2152,8 +2188,8 @@ 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: 2382.94 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1237.49 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2214,7 +2250,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1685.80 +# Mc/sec: 982.73 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2264,8 +2300,8 @@ 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: 1502.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 141.30 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2377,8 +2413,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1326.69 +# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 520.70 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2425,7 +2461,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2402.35 +# Mc/sec: 1384.15 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2492,7 +2528,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2159.33 +# Mc/sec: 1171.40 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2531,7 +2567,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 4192.23 +# Mc/sec: 2330.61 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2607,8 +2643,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1700.96 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 691.86 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2660,8 +2696,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2581.75 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1529.06 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2745,8 +2781,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 584.06 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 199.23 // Query: DLH [M=217] Accession: PF01738.17 @@ -2794,7 +2830,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3698.14 +# Mc/sec: 1760.58 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2841,7 +2877,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2044.65 +# Mc/sec: 1202.44 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2890,8 +2926,8 @@ 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: 3383.50 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1785.00 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2933,8 +2969,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3506.30 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2005.14 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -2980,7 +3016,7 @@ 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: 1494.04 +# Mc/sec: 660.76 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3018,7 +3054,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3571.59 +# Mc/sec: 2025.50 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3069,8 +3105,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1824.77 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 960.10 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3108,7 +3144,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1900.51 +# Mc/sec: 1205.62 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3146,7 +3182,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3267.08 +# Mc/sec: 1884.93 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3197,7 +3233,7 @@ 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: 2561.92 +# Mc/sec: 1389.83 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3235,7 +3271,7 @@ 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: 4533.29 +# Mc/sec: 2355.14 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3296,7 +3332,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2578.90 +# Mc/sec: 1403.61 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3341,7 +3377,7 @@ 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: 2745.06 +# Mc/sec: 1512.54 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3397,8 +3433,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2736.73 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 908.14 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3452,8 +3488,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1036.14 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 403.57 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3491,7 +3527,7 @@ 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: 4267.27 +# Mc/sec: 2170.59 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3568,7 +3604,7 @@ 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: 2850.69 +# Mc/sec: 1500.30 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3632,8 +3668,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 906.08 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 329.82 // Query: FPP [M=866] Accession: PF05911.10 @@ -3683,8 +3719,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2387.18 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 1024.74 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3736,8 +3772,8 @@ 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: 2670.56 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.15 +# Mc/sec: 17.77 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3860,8 +3896,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 763.25 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 331.53 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3900,7 +3936,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2016.88 +# Mc/sec: 1062.86 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -3990,8 +4026,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 929.85 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 385.73 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4041,8 +4077,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 693.36 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 206.93 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4102,8 +4138,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1758.23 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 881.63 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4208,7 +4244,7 @@ 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: 991.81 +# Mc/sec: 428.82 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4255,8 +4291,8 @@ 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: 2477.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1505.08 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4330,8 +4366,8 @@ 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: 1594.86 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 839.96 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4401,8 +4437,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2206.03 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1201.22 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4449,8 +4485,8 @@ 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: 1202.05 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 472.93 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4520,8 +4556,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 422.76 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 159.85 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4571,8 +4607,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3484.94 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1857.47 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4623,7 +4659,7 @@ 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: 3644.59 +# Mc/sec: 1980.11 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4661,8 +4697,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2653.52 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1338.62 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4707,7 +4743,7 @@ 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: 2195.15 +# Mc/sec: 1333.17 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4759,7 +4795,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1835.94 +# Mc/sec: 1048.25 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4841,8 +4877,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1327.55 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 769.80 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4942,8 +4978,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 991.33 +# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 +# Mc/sec: 315.64 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -4998,7 +5034,7 @@ 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: 1804.24 +# Mc/sec: 839.27 // Query: IBR [M=62] Accession: PF01485.20 @@ -5036,7 +5072,7 @@ 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: 2107.64 +# Mc/sec: 1070.08 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5083,8 +5119,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1407.68 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 487.08 // Query: malic [M=182] Accession: PF00390.18 @@ -5123,7 +5159,7 @@ 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: 4058.81 +# Mc/sec: 2057.87 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5160,8 +5196,8 @@ 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: 1565.73 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 658.51 // Query: MatE [M=161] Accession: PF01554.17 @@ -5245,8 +5281,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1698.99 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.13 +# Mc/sec: 38.04 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5283,8 +5319,8 @@ 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: 3831.30 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1276.35 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5458,8 +5494,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 289.85 +# CPU time: 0.10u 0.00s 00:00:00.10 Elapsed: 00:00:00.10 +# Mc/sec: 105.50 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5501,8 +5537,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2507.85 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1034.79 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5558,8 +5594,8 @@ 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: 1454.83 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 +# Mc/sec: 420.98 // Query: MIP [M=227] Accession: PF00230.19 @@ -5609,8 +5645,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3057.86 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1404.33 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5662,8 +5698,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1760.04 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 843.86 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5753,8 +5789,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2569.43 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1130.83 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5792,7 +5828,7 @@ 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: 2408.16 +# Mc/sec: 1070.45 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5829,8 +5865,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3822.58 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1907.59 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5883,7 +5919,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3040.99 +# Mc/sec: 1322.73 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5921,7 +5957,7 @@ 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: 4428.56 +# Mc/sec: 1959.04 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6041,8 +6077,8 @@ 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: 1260.93 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 478.22 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6092,8 +6128,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3072.80 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1401.43 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6164,7 +6200,7 @@ 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: 2653.81 +# Mc/sec: 1200.26 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6216,8 +6252,8 @@ 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: 1330.00 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 551.63 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6279,8 +6315,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2109.99 +# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 +# Mc/sec: 899.63 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6382,8 +6418,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 359.57 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 136.17 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6431,7 +6467,7 @@ 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: 2640.14 +# Mc/sec: 1083.69 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6482,7 +6518,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1683.97 +# Mc/sec: 804.17 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6533,7 +6569,7 @@ 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: 2507.66 +# Mc/sec: 1262.93 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6583,8 +6619,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3643.18 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1903.13 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6629,7 +6665,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3403.07 +# Mc/sec: 1693.26 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6675,8 +6711,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1584.56 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 730.47 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6740,8 +6776,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 742.11 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 279.84 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6786,7 +6822,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2389.84 +# Mc/sec: 1033.56 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6838,8 +6874,8 @@ 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: 1244.66 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 451.93 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6884,7 +6920,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3305.86 +# Mc/sec: 1495.86 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -6984,8 +7020,8 @@ 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: 681.94 +# CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 +# Mc/sec: 226.85 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7029,8 +7065,8 @@ 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: 958.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 360.70 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7083,7 +7119,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2674.50 +# Mc/sec: 1485.41 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7156,8 +7192,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 539.97 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 +# Mc/sec: 210.05 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7217,8 +7253,8 @@ 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: 2383.84 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1251.38 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7263,7 +7299,7 @@ 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: 2666.26 +# Mc/sec: 1068.04 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7316,7 +7352,7 @@ 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: 2578.81 +# Mc/sec: 1336.73 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7353,8 +7389,8 @@ 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: 6486.80 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2518.04 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7397,7 +7433,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3477.17 +# Mc/sec: 1673.81 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7459,8 +7495,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 932.10 +# CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 +# Mc/sec: 369.40 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7498,7 +7534,7 @@ 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: 3729.30 +# Mc/sec: 1987.72 // Query: Usher [M=551] Accession: PF00577.19 @@ -7542,8 +7578,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3077.52 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1328.17 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7590,7 +7626,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1009.88 +# Mc/sec: 427.40 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7634,8 +7670,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1042.98 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 466.79 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7679,8 +7715,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1101.39 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.12 +# Mc/sec: 6.51 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7735,7 +7771,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1240.40 +# Mc/sec: 408.74 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7774,7 +7810,7 @@ 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: 828.09 +# Mc/sec: 311.27 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7826,7 +7862,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1139.37 +# Mc/sec: 415.05 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7874,7 +7910,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1879.35 +# Mc/sec: 750.34 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7913,14 +7949,14 @@ 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: 1635.34 +# Mc/sec: 679.87 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Mon Jun 9 04:22:35 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 Jun 9 04:22:35 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 +* [Wed May 8 00:10:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed May 8 00:10:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: CUFF.60.1.p1, not unique enough -skipping training candidate: CUFF.26.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p3, not unique enough @@ -7947,39 +7983,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Mon Jun 9 04:22:35 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 +* [Wed May 8 00:10:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:22:35 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 Jun 9 04:22:35 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 Jun 9 04:22:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed May 8 00:10:41 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 +* [Wed May 8 00:10:41 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 +* [Wed May 8 00:10:43 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 Jun 9 04:22:36 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 Jun 9 04:22:36 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 Jun 9 04:22:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed May 8 00:10:44 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* [Wed May 8 00:10:44 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 +* [Wed May 8 00:10:44 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 Jun 9 04:22:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Wed May 8 00:11:41 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/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 Jun 9 04:22:59 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 || : +* [Wed May 8 00:11:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:23:00 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 +* [Wed May 8 00:11:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Jun 9 04:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed May 8 00:11:55 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 Jun 9 04:23:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed May 8 00:11:56 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:23:02 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 +* [Wed May 8 00:11:58 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 -feature swap of score: 1.94858034627835 instead of -0.884029553505083 @@ -7989,33 +8025,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Mon Jun 9 04:23:02 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 +* [Wed May 8 00:11:58 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 Jun 9 04:23:20 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 +* [Wed May 8 00:12:51 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 Jun 9 04:23:24 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 || : +* [Wed May 8 00:13:00 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:23:25 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 +* [Wed May 8 00:13:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Mon Jun 9 04:23:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed May 8 00:13:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:23:27 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 +* [Wed May 8 00:13:06 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 Jun 9 04:23:27 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 Jun 9 04:23:27 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 +* [Wed May 8 00:13:06 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* [Wed May 8 00:13:06 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 Jun 9 04:23:27 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 +* [Wed May 8 00:13:06 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 Jun 9 04:23:27 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 +* [Wed May 8 00:13:06 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* @@ -8107,7 +8143,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Mon Jun 9 04:23:27 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 +* [Wed May 8 00:13:07 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -8131,8 +8167,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Mon Jun 9 04:23:29 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/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 Jun 9 04:23:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:13:12 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 May 8 00:13:13 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough @@ -8807,37 +8843,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Mon Jun 9 04:23:30 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 May 8 00:13:14 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:23:30 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 Jun 9 04:23:31 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 Jun 9 04:23:37 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 May 8 00:13:14 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/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 May 8 00:13:16 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 May 8 00:13:31 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 Jun 9 04:23:37 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 Jun 9 04:23:37 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 Jun 9 04:23:37 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 May 8 00:13:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Wed May 8 00:13:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Wed May 8 00:13:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon Jun 9 04:24:06 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 May 8 00:14:49 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:24:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Wed May 8 00:15:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:24:14 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed May 8 00:15:04 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Jun 9 04:24:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed May 8 00:15:06 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 Jun 9 04:24:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed May 8 00:15:07 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:24:17 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 May 8 00:15:08 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 @@ -8896,33 +8932,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Mon Jun 9 04:24:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:15:09 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 Jun 9 04:24:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed May 8 00:16:23 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 Jun 9 04:25:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed May 8 00:16:37 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:25:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed May 8 00:16:39 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 Jun 9 04:25:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed May 8 00:16:41 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.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:25:09 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 May 8 00:16:42 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 Jun 9 04:25:10 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 Jun 9 04:25:10 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 May 8 00:16:43 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 May 8 00:16:43 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 Jun 9 04:25:10 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 May 8 00:16:43 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 Jun 9 04:25:11 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/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 May 8 00:16:44 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* @@ -8979,8 +9015,8 @@ CDS coords: 80, 427 -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). --Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. --Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 112, 447 @@ -9015,7 +9051,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Mon Jun 9 04:25:12 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 May 8 00:16:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -9035,8 +9071,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Mon Jun 9 04:25:15 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 Jun 9 04:25:15 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 May 8 00:16:50 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 May 8 00:16:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0_seq2.p1, not unique enough -skipping training candidate: comp992_c0_seq2.p1, not unique enough -skipping training candidate: comp718_c0_seq2.p1, not unique enough @@ -9074,37 +9110,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Mon Jun 9 04:25:17 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 May 8 00:16:51 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 Jun 9 04:25:17 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 Jun 9 04:25:19 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 Jun 9 04:25:25 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/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 May 8 00:16:52 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 May 8 00:16:57 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 May 8 00:17:11 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 Jun 9 04:25:25 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 Jun 9 04:25:25 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 Jun 9 04:25:26 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/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 May 8 00:17:11 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 May 8 00:17:11 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 May 8 00:17:13 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 Jun 9 04:26:07 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/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 May 8 00:18:26 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/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 Jun 9 04:26:14 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 May 8 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/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:26:15 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 May 8 00:18:43 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 Jun 9 04:26:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed May 8 00:18:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:26:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed May 8 00:18:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:26:17 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 May 8 00:18:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 @@ -9210,33 +9246,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Mon Jun 9 04:26:18 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 May 8 00:18:49 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 Jun 9 04:26:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.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 May 8 00:20:18 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.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 Jun 9 04:26:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed May 8 00:20:33 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 Jun 9 04:26:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed May 8 00:20:35 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 Jun 9 04:26:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed May 8 00:20:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon Jun 9 04:26:57 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 May 8 00:20:39 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 Jun 9 04:26:57 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 Jun 9 04:26:57 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 May 8 00:20:39 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 May 8 00:20:39 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 Jun 9 04:26:58 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/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 May 8 00:20:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:26:59 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 May 8 00:20:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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.* @@ -9260,25 +9296,25 @@ '1644586' ] ], + 'gene_id' => '', 'asmbl' => 'comp1051_c1_seq1', 'contig' => 'III', - 'trans_id' => '', - 'gene_id' => '' + 'trans_id' => '' }; + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + source: transdecoder + strand: + + asmbl_id: comp1051_c1_seq1 num_exons: 1 + gene_type: protein-coding + is_3prime_partial: 0 is_pseudogene: 0 - gene_length: 1616 com_name: ORF type:5prime_partial (+),score=83.26 + mid_pt: 808 Model_feat_name: comp1051_c1_seq1.p1 - strand: + - asmbl_id: comp1051_c1_seq1 + gene_length: 1616 classification: annotated_genes - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 is_5prime_partial: 0 - mid_pt: 808 - is_3prime_partial: 0 - gene_type: protein-coding - source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9295,8 +9331,8 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'I', - 'asmbl' => 'comp1058_c0_seq1', + 'orient' => '-', + 'gene_id' => '', 'coords' => [ [ 5095548, @@ -9307,24 +9343,24 @@ '5095301' ] ], - 'orient' => '-', - 'gene_id' => '', - 'trans_id' => '' + 'trans_id' => '', + 'asmbl' => 'comp1058_c0_seq1', + 'contig' => 'I' }; - strand: + - Model_feat_name: comp1058_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=32.57 - gene_length: 496 is_pseudogene: 0 - num_exons: 1 - source: transdecoder - gene_type: protein-coding is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=32.57 + Model_feat_name: comp1058_c0_seq1.p1 mid_pt: 248 is_5prime_partial: 0 - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 classification: annotated_genes + gene_length: 496 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + source: transdecoder asmbl_id: comp1058_c0_seq1 + strand: + + gene_type: protein-coding + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9348,8 +9384,7 @@ Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'orient' => '-', - 'contig' => 'III', - 'asmbl' => 'comp1112_c0_seq1', + 'gene_id' => '', 'coords' => [ [ 2380416, @@ -9361,22 +9396,23 @@ ] ], 'trans_id' => '', - 'gene_id' => '' + 'asmbl' => 'comp1112_c0_seq1', + 'contig' => 'III' }; - asmbl_id: comp1112_c0_seq1 + com_name: ORF type:complete (+),score=155.28 + is_pseudogene: 0 + is_3prime_partial: 0 + classification: annotated_genes + gene_length: 2081 is_5prime_partial: 0 - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 mid_pt: 1041 - classification: annotated_genes - is_3prime_partial: 0 - gene_type: protein-coding + Model_feat_name: comp1112_c0_seq1.p1 source: transdecoder - is_pseudogene: 0 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 num_exons: 1 - gene_length: 2081 - com_name: ORF type:complete (+),score=155.28 - Model_feat_name: comp1112_c0_seq1.p1 + gene_type: protein-coding strand: + + asmbl_id: comp1112_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9398,8 +9434,8 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp1198_c0_seq1', - 'contig' => 'II', + 'orient' => '-', + 'gene_id' => '', 'coords' => [ [ 402195, @@ -9418,24 +9454,24 @@ '401683' ] ], - 'orient' => '-', - 'gene_id' => '', - 'trans_id' => '' + 'trans_id' => '', + 'contig' => 'II', + 'asmbl' => 'comp1198_c0_seq1' }; - asmbl_id: comp1198_c0_seq1 is_3prime_partial: 0 + is_pseudogene: 0 + com_name: ORF type:internal (+),score=37.56 mid_pt: 299 - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - is_5prime_partial: 0 + Model_feat_name: comp1198_c0_seq1.p1 classification: annotated_genes - gene_type: protein-coding - source: transdecoder - is_pseudogene: 0 - num_exons: 1 gene_length: 597 - Model_feat_name: comp1198_c0_seq1.p1 - com_name: ORF type:internal (+),score=37.56 + is_5prime_partial: 0 + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + source: transdecoder strand: + + asmbl_id: comp1198_c0_seq1 + num_exons: 1 + gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9464,9 +9500,6 @@ Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', - 'trans_id' => '', - 'contig' => 'III', - 'asmbl' => 'comp1210_c0_seq1', 'coords' => [ [ 368840, @@ -9477,22 +9510,25 @@ '368790' ] ], + 'trans_id' => '', + 'asmbl' => 'comp1210_c0_seq1', + 'contig' => 'III', 'orient' => '-' }; - Model_feat_name: comp1210_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=12.16 + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + source: transdecoder + asmbl_id: comp1210_c0_seq1 strand: + + gene_type: protein-coding num_exons: 1 is_pseudogene: 0 - gene_length: 1554 - gene_type: protein-coding - source: transdecoder - asmbl_id: comp1210_c0_seq1 is_3prime_partial: 0 - classification: annotated_genes - is_5prime_partial: 0 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=12.16 + Model_feat_name: comp1210_c0_seq1.p1 mid_pt: 777 + is_5prime_partial: 0 + classification: annotated_genes + gene_length: 1554 gene_synonyms: mRNA_coords CDS_coords @@ -9517,32 +9553,32 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '-', 'coords' => [ [ '3840968', '3841303' ] ], + 'gene_id' => '', 'asmbl' => 'comp366_c0_seq1', 'contig' => 'II', - 'orient' => '-', - 'gene_id' => '', 'trans_id' => '' }; - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - is_5prime_partial: 0 + Model_feat_name: comp366_c0_seq1.p1 mid_pt: 170 + is_5prime_partial: 0 classification: annotated_genes + gene_length: 340 is_3prime_partial: 0 + is_pseudogene: 0 + com_name: ORF type:internal (-),score=12.83 asmbl_id: comp366_c0_seq1 - source: transdecoder + strand: - gene_type: protein-coding - gene_length: 340 - is_pseudogene: 0 num_exons: 1 - strand: - - com_name: ORF type:internal (-),score=12.83 - Model_feat_name: comp366_c0_seq1.p1 + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + source: transdecoder gene_synonyms: mRNA_coords CDS_coords @@ -9568,7 +9604,8 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'asmbl' => 'comp610_c0_seq1', + 'contig' => 'I', 'trans_id' => '', 'coords' => [ [ @@ -9576,24 +9613,23 @@ '5472770' ] ], - 'asmbl' => 'comp610_c0_seq1', - 'contig' => 'I', + 'gene_id' => '', 'orient' => '-' }; - classification: annotated_genes - is_5prime_partial: 0 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - mid_pt: 755 - is_3prime_partial: 0 - asmbl_id: comp610_c0_seq1 - source: transdecoder gene_type: protein-coding - gene_length: 1509 num_exons: 1 - is_pseudogene: 0 + asmbl_id: comp610_c0_seq1 strand: + - com_name: ORF type:5prime_partial (+),score=50.55 + source: transdecoder + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + is_5prime_partial: 0 + gene_length: 1509 + classification: annotated_genes Model_feat_name: comp610_c0_seq1.p1 + mid_pt: 755 + com_name: ORF type:5prime_partial (+),score=50.55 + is_3prime_partial: 0 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9612,32 +9648,32 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'contig' => 'I', + 'asmbl' => 'comp645_c0_seq1', 'trans_id' => '', - 'gene_id' => '', - 'orient' => '-', 'coords' => [ [ '4333088', '4336727' ] ], - 'contig' => 'I', - 'asmbl' => 'comp645_c0_seq1' + 'gene_id' => '', + 'orient' => '-' }; source: transdecoder - gene_type: protein-coding - mid_pt: 1827 - is_5prime_partial: 0 TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 - classification: annotated_genes - is_3prime_partial: 0 + gene_type: protein-coding + num_exons: 1 asmbl_id: comp645_c0_seq1 strand: + com_name: ORF type:5prime_partial (+),score=273.35 - Model_feat_name: comp645_c0_seq1.p1 - gene_length: 3653 + is_3prime_partial: 0 is_pseudogene: 0 - num_exons: 1 + is_5prime_partial: 0 + gene_length: 3653 + classification: annotated_genes + Model_feat_name: comp645_c0_seq1.p1 + mid_pt: 1827 gene_synonyms: mRNA_coords CDS_coords @@ -9653,8 +9689,10 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'trans_id' => '', + 'asmbl' => 'comp688_c0_seq1', + 'contig' => 'II', + 'gene_id' => '', 'coords' => [ [ 380308, @@ -9665,24 +9703,22 @@ '381243' ] ], - 'asmbl' => 'comp688_c0_seq1', - 'contig' => 'II', 'orient' => '+' }; - source: transdecoder - gene_type: protein-coding - classification: annotated_genes is_5prime_partial: 0 - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + gene_length: 2784 + classification: annotated_genes + Model_feat_name: comp688_c0_seq1.p1 mid_pt: 1392 + com_name: ORF type:complete (+),score=172.54 + is_pseudogene: 0 is_3prime_partial: 0 + gene_type: protein-coding + num_exons: 1 asmbl_id: comp688_c0_seq1 strand: + - com_name: ORF type:complete (+),score=172.54 - Model_feat_name: comp688_c0_seq1.p1 - gene_length: 2784 - num_exons: 1 - is_pseudogene: 0 + source: transdecoder + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9706,8 +9742,10 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp856_c0_seq1', + 'trans_id' => '', 'contig' => 'II', + 'asmbl' => 'comp856_c0_seq1', + 'gene_id' => '', 'coords' => [ [ 3753910, @@ -9718,23 +9756,21 @@ '3755057' ] ], - 'orient' => '+', - 'gene_id' => '', - 'trans_id' => '' + 'orient' => '+' }; - gene_type: protein-coding + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 source: transdecoder asmbl_id: comp856_c0_seq1 - mid_pt: 785 - is_5prime_partial: 0 - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 - classification: annotated_genes + strand: + + gene_type: protein-coding + num_exons: 1 + is_pseudogene: 0 is_3prime_partial: 0 com_name: ORF type:complete (+),score=71.94 Model_feat_name: comp856_c0_seq1.p1 - strand: + - is_pseudogene: 0 - num_exons: 1 + mid_pt: 785 + is_5prime_partial: 0 + classification: annotated_genes gene_length: 1569 gene_synonyms: mRNA_coords @@ -9755,7 +9791,9 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'orient' => '-', + 'asmbl' => 'comp873_c0_seq2', + 'contig' => 'II', 'trans_id' => '', 'coords' => [ [ @@ -9771,24 +9809,22 @@ '3727657' ] ], - 'contig' => 'II', - 'asmbl' => 'comp873_c0_seq2', - 'orient' => '-' + 'gene_id' => '' }; source: transdecoder - gene_type: protein-coding - is_3prime_partial: 0 - classification: annotated_genes - mid_pt: 513 - is_5prime_partial: 0 TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + gene_type: protein-coding + num_exons: 1 asmbl_id: comp873_c0_seq2 strand: + - Model_feat_name: comp873_c0_seq2.p1 com_name: ORF type:5prime_partial (+),score=8.59 - gene_length: 1025 - num_exons: 1 + is_3prime_partial: 0 is_pseudogene: 0 + is_5prime_partial: 0 + gene_length: 1025 + classification: annotated_genes + Model_feat_name: comp873_c0_seq2.p1 + mid_pt: 513 gene_synonyms: mRNA_coords CDS_coords @@ -9813,6 +9849,9 @@ Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'orient' => '-', + 'asmbl' => 'comp888_c0_seq1', + 'contig' => 'III', + 'trans_id' => '', 'coords' => [ [ 1268244, @@ -9823,25 +9862,22 @@ '1268172' ] ], - 'contig' => 'III', - 'asmbl' => 'comp888_c0_seq1', - 'trans_id' => '', 'gene_id' => '' }; - asmbl_id: comp888_c0_seq1 - is_3prime_partial: 0 - classification: annotated_genes - mid_pt: 295 is_5prime_partial: 0 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 - gene_type: protein-coding - source: transdecoder - num_exons: 1 - is_pseudogene: 0 gene_length: 589 + classification: annotated_genes Model_feat_name: comp888_c0_seq1.p1 + mid_pt: 295 com_name: ORF type:5prime_partial (+),score=23.94 + is_3prime_partial: 0 + is_pseudogene: 0 + gene_type: protein-coding + num_exons: 1 + asmbl_id: comp888_c0_seq1 strand: + + source: transdecoder + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9863,6 +9899,10 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '+', + 'asmbl' => 'comp940_c0_seq1', + 'contig' => 'III', + 'trans_id' => '', 'coords' => [ [ 105641, @@ -9873,26 +9913,22 @@ '106404' ] ], - 'contig' => 'III', - 'asmbl' => 'comp940_c0_seq1', - 'orient' => '+', - 'gene_id' => '', - 'trans_id' => '' + 'gene_id' => '' }; - is_5prime_partial: 0 - TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 - mid_pt: 1065 - classification: annotated_genes - is_3prime_partial: 0 - asmbl_id: comp940_c0_seq1 source: transdecoder + TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 gene_type: protein-coding - gene_length: 2129 - is_pseudogene: 0 num_exons: 1 + asmbl_id: comp940_c0_seq1 strand: + com_name: ORF type:complete (+),score=94.37 + is_3prime_partial: 0 + is_pseudogene: 0 + is_5prime_partial: 0 + gene_length: 2129 + classification: annotated_genes Model_feat_name: comp940_c0_seq1.p1 + mid_pt: 1065 gene_synonyms: mRNA_coords CDS_coords @@ -9912,9 +9948,10 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'gene_id' => '', 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp983_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 4100066, @@ -9925,23 +9962,22 @@ '4100014' ] ], - 'asmbl' => 'comp983_c0_seq1', - 'contig' => 'I' + 'gene_id' => '' }; - gene_length: 1870 - num_exons: 1 - is_pseudogene: 0 strand: + + asmbl_id: comp983_c0_seq1 + num_exons: 1 + gene_type: protein-coding + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + source: transdecoder + mid_pt: 935 Model_feat_name: comp983_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=143.65 - is_3prime_partial: 0 classification: annotated_genes - mid_pt: 935 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + gene_length: 1870 is_5prime_partial: 0 - asmbl_id: comp983_c0_seq1 - source: transdecoder - gene_type: protein-coding + is_pseudogene: 0 + is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=143.65 gene_synonyms: mRNA_coords CDS_coords @@ -9985,7 +10021,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Mon Jun 9 04:27:01 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 May 8 00:20:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -10010,8 +10046,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Mon Jun 9 04:27:14 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 Jun 9 04:27:14 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 May 8 00:21:13 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/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 May 8 00:21:15 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: NM_198270.p1, not unique enough -skipping training candidate: NR_104391.p1, not unique enough -skipping training candidate: NR_104395.p1, not unique enough @@ -12629,37 +12665,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Mon Jun 9 04:27:17 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 May 8 00:21:19 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Mon Jun 9 04:27:17 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 Jun 9 04:27:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:27:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Wed May 8 00:21:20 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores +* [Wed May 8 00:21:26 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 May 8 00:23:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Mon Jun 9 04:27:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Jun 9 04:27:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Jun 9 04:27:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:23:04 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 May 8 00:23:04 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 May 8 00:23:07 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.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 Jun 9 04:28:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:24:32 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 Jun 9 04:28:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Wed May 8 00:24:46 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 Jun 9 04:28:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed May 8 00:24:49 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 Jun 9 04:28:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed May 8 00:24:51 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 Jun 9 04:28:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Wed May 8 00:24:52 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 Jun 9 04:28:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:24:54 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 @@ -12720,7 +12756,7 @@ -feature swap of score: 3.99301668862372 instead of 1.24561259795263 -feature swap of score: 1.72372236527001 instead of 1.02241527158741 -feature swap of score: 6.86300883201794 instead of 1.14563582053961 --feature swap of score: 5.54190533772704 instead of 1.28297492173032 +-feature swap of score: 5.54190533772704 instead of 1.28297492173033 -feature swap of score: 2.51308026289154 instead of 1.4180584754329 -feature swap of score: 3.38846514773249 instead of 1.2857641622143 -feature swap of score: 2.49385651598659 instead of 1.55130322997112 @@ -12762,33 +12798,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Mon Jun 9 04:28:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:24:55 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 Jun 9 04:29:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:26:30 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.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 Jun 9 04:29:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Wed May 8 00:26:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:29:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Wed May 8 00:26:47 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 Jun 9 04:29:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed May 8 00:26:49 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 Jun 9 04:29:33 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 May 8 00:26:50 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 Jun 9 04:29:35 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 Jun 9 04:29:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:26:53 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 May 8 00:26:53 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 Jun 9 04:29:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:26:55 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 Jun 9 04:29:38 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 May 8 00:26:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* @@ -12900,7 +12936,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Mon Jun 9 04:29:47 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 May 8 00:27:18 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -12924,10 +12960,10 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Mon Jun 9 04:29:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:29:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:27:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:27:23 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -12935,8 +12971,8 @@ -skipping training candidate: eIF5B_i4.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough --skipping training candidate: Dgk_i3.p1, not unique enough -skipping training candidate: Dgk_i6.p1, not unique enough +-skipping training candidate: Dgk_i3.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough @@ -12946,36 +12982,36 @@ -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough --skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i5.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_i4.p1, not unique enough +-skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough --skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough --skipping training candidate: Klp10A_i3.p1, not unique enough --skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough +-skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: Klp10A_i6.p1, not unique enough -skipping training candidate: Klp10A_i1.p1, not unique enough -skipping training candidate: Klp10A_i5.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough --skipping training candidate: CG33970_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_i3.p1, not unique enough +-skipping training candidate: CG6091_i1.p1, not unique enough +-skipping training candidate: hrg_i3.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: hrg_i2.p1, not unique enough --skipping training candidate: hrg_i3.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough --skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough +-skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough @@ -12987,99 +13023,99 @@ -skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough +-skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough --skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Est-6_i2.p1, not unique enough --skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: S-Lap3_i1.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_i5.p1, not unique enough -skipping training candidate: CG30438_i3.p1, not unique enough +-skipping training candidate: CG30438_i2.p1, not unique enough -skipping training candidate: 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_i5.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_i1.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough --skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i6.p1, not unique enough -skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i4.p1, not unique enough --skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough +-skipping training candidate: Aldh-III_i8.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough --skipping training candidate: Eno_i3.p2, not unique enough --skipping training candidate: Eno_i5.p2, not unique enough --skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough +-skipping training candidate: Eno_i5.p2, not unique enough +-skipping training candidate: Eno_i3.p2, not unique enough -skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: CG6424_i1.p2, not unique enough +-skipping training candidate: CG6424_i2.p2, not unique enough -skipping training candidate: CG6424_i4.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough --skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Irk2_i4.p1, not unique enough +-skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough -skipping training candidate: AdipoR_i2.p1, not unique enough -skipping training candidate: AdipoR_i4.p1, not unique enough --skipping training candidate: AdipoR_i5.p1, not unique enough +-skipping training candidate: AdipoR_i3.p1, not unique enough -skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough --skipping training candidate: kto_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_i3.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_i3.p1, not unique enough +-skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG7564_i1.p1, not unique enough --skipping training candidate: CG7564_i4.p1, not unique enough +-skipping training candidate: CG7564_i3.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough -skipping training candidate: nmo_i4.p1, not unique enough --skipping training candidate: nmo_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: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough --skipping training candidate: CG6024_i2.p1, not unique enough +-skipping training candidate: CG6024_i1.p1, not unique enough -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough --skipping training candidate: ogre_i6.p1, not unique enough --skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i1.p1, not unique enough -skipping training candidate: ogre_i5.p1, not unique enough --skipping training candidate: ogre_i3.p1, not unique enough -skipping training candidate: ogre_i4.p1, not unique enough +-skipping training candidate: ogre_i3.p1, not unique enough +-skipping training candidate: ogre_i2.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough --skipping training candidate: Gale_i1.p1, not unique enough +-skipping training candidate: Gale_i2.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough --skipping training candidate: CG13284_i5.p1, not unique enough +-skipping training candidate: CG13284_i3.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough -skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough --skipping training candidate: Klp10A_i3.p2, not unique enough --skipping training candidate: Klp10A_i2.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_i6.p2, not unique enough -skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Klp10A_i5.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough @@ -13088,531 +13124,535 @@ -skipping training candidate: CG10237_i5.p1, not unique enough -skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough +-skipping training candidate: regucalcin_i4.p1, not unique enough -skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough --skipping training candidate: regucalcin_i4.p1, not unique enough --skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough +-skipping training candidate: CG10237_i3.p1, not unique enough +-skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: l(3)05822_i3.p2, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough --skipping training candidate: l(3)05822_i2.p2, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough --skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Tm1_i11.p1, not unique enough +-skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough --skipping training candidate: Npl4_i3.p2, not unique enough +-skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Npl4_i1.p2, not unique enough +-skipping training candidate: Npl4_i3.p2, not unique enough +-skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough --skipping training candidate: Sec16_i1.p2, not unique enough --skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough +-skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i3.p2, not unique enough -skipping training candidate: eIF5B_i5.p2, not unique enough +-skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: eIF5B_i3.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_i6.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough -skipping training candidate: Dgk_i3.p2, not unique enough --skipping training candidate: Dgk_i6.p2, not unique enough --skipping training candidate: l(1)G0193_i1.p2, not unique enough +-skipping training candidate: l(1)G0193_i2.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -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_i3.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough -skipping training candidate: Dgk_i6.p3, not unique enough +-skipping training candidate: Dgk_i2.p3, not unique enough +-skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: l(3)05822_i4.p3, not unique enough -skipping training candidate: l(3)05822_i3.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough --skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough --skipping training candidate: CG6024_i2.p2, not unique enough --skipping training candidate: Sec16_i2.p3, not unique enough +-skipping training candidate: CG6024_i1.p2, not unique enough -skipping training candidate: Sec16_i6.p2, not unique enough --skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough +-skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG14995_i7.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough --skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i3.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_i7.p2, not unique enough +-skipping training candidate: nmo_i2.p2, not unique enough +-skipping training candidate: nmo_i6.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough --skipping training candidate: gukh_i1.p2, not unique enough +-skipping training candidate: gukh_i4.p3, not unique enough -skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough +-skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough --skipping training candidate: RpL15_i1.p1, not unique enough --skipping training candidate: RpL15_i5.p1, not unique enough -skipping training candidate: RpL15_i3.p1, not unique enough --skipping training candidate: RpL15_i2.p1, not unique enough --skipping training candidate: Npl4_i3.p3, not unique enough +-skipping training candidate: RpL15_i5.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: trc_i1.p2, not unique enough +-skipping training candidate: Npl4_i3.p3, not unique enough +-skipping training candidate: trc_i2.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough -skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough +-skipping training candidate: CG10237_i1.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough -skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: CG10237_i4.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough -skipping training candidate: Eno_i5.p3, not unique enough --skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i6.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_i1.p3, not unique enough +-skipping training candidate: Eno_i6.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough +-skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough --skipping training candidate: Sec16_i1.p3, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough --skipping training candidate: gukh_i2.p2, not unique enough +-skipping training candidate: gukh_i1.p3, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough -skipping training candidate: ATPsyn-d_i3.p1, not unique enough --skipping training candidate: CG10082_i1.p2, not unique enough +-skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough --skipping training candidate: CG30438_i2.p2, not unique enough +-skipping training candidate: CG30438_i1.p2, not unique enough -skipping training candidate: CG30438_i5.p2, not unique enough -skipping training candidate: CG30438_i3.p2, not unique enough --skipping training candidate: CG30438_i4.p2, not unique enough +-skipping training candidate: CG30438_i2.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough --skipping training candidate: cdi_i2.p2, not unique enough +-skipping training candidate: cdi_i1.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i2.p1, not unique enough -skipping training candidate: ADD1_i3.p2, not unique enough +-skipping training candidate: Sec16_i3.p3, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: Sec16_i1.p4, not unique enough -skipping training candidate: bic_i2.p1, not unique enough -skipping training candidate: CG12581_i2.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough +-skipping training candidate: ctp_i2.p1, not unique enough -skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: ctp_i1.p1, not unique enough --skipping training candidate: ctp_i4.p1, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: Eno_i5.p4, not unique enough --skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: Eno_i3.p4, not unique enough -skipping training candidate: Eno_i1.p4, not unique enough --skipping training candidate: Klp10A_i3.p3, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Eno_i6.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Klp10A_i5.p3, 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_i5.p2, not unique enough +-skipping training candidate: Calx_i2.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough -skipping training candidate: Calx_i3.p2, not unique enough -skipping training candidate: Calx_i4.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_i8.p2, not unique enough -skipping training candidate: Calx_i9.p2, not unique enough --skipping training candidate: Calx_i2.p2, not unique enough +-skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough +-skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough --skipping training candidate: CG7564_i4.p2, not unique enough --skipping training candidate: CG7564_i4.p3, not unique enough --skipping training candidate: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: CG7564_i3.p3, not unique enough +-skipping training candidate: Gale_i2.p2, not unique enough -skipping training candidate: eIF5B_i5.p3, not unique enough +-skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i3.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_i2.p3, not unique enough +-skipping training candidate: AdipoR_i3.p2, not unique enough -skipping training candidate: CG6424_i1.p3, not unique enough -skipping training candidate: CG6424_i1.p4, not unique enough +-skipping training candidate: CG6424_i2.p3, not unique enough -skipping training candidate: CG6424_i4.p3, not unique enough +-skipping training candidate: Tm1_i16.p2, not unique enough -skipping training candidate: Tm1_i13.p2, not unique enough --skipping training candidate: Tm1_i5.p2, not unique enough -skipping training candidate: Tm1_i14.p2, not unique enough --skipping training candidate: Dgk_i7.p5, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough -skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Dgk_i2.p5, not unique enough -skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: cdi_i2.p3, not unique enough --skipping training candidate: eff_i3.p1, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: cdi_i1.p4, not unique enough -skipping training candidate: eff_i1.p1, not unique enough +-skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i3.p4, not unique enough -skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: eIF5B_i2.p4, not unique enough +-skipping training candidate: eIF5B_i3.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_i5.p4, not unique enough --skipping training candidate: Sec16_i2.p5, not unique enough --skipping training candidate: Sec16_i4.p5, not unique enough --skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough --skipping training candidate: CG32082_i2.p2, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: Sec16_i4.p5, not unique enough +-skipping training candidate: Sec16_i2.p5, not unique enough +-skipping training candidate: CG32082_i1.p2, not unique enough -skipping training candidate: CG32082_i3.p2, not unique enough --skipping training candidate: CG32082_i4.p2, not unique enough --skipping training candidate: CG3530_i2.p2, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough +-skipping training candidate: CG3530_i1.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough --skipping training candidate: Dgk_i7.p6, not unique enough +-skipping training candidate: Dgk_i2.p6, not unique enough +-skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough --skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: sqd_i1.p2, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough +-skipping training candidate: CG7564_i2.p6, not unique enough -skipping training candidate: CG7564_i1.p4, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough --skipping training candidate: S-Lap3_i2.p2, not unique enough +-skipping training candidate: CG7564_i3.p4, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough --skipping training candidate: cdi_i2.p4, not unique enough --skipping training candidate: CG6091_i4.p2, not unique enough --skipping training candidate: CG6091_i3.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: CG6091_i2.p2, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough +-skipping training candidate: CG6091_i4.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough --skipping training candidate: Cnx99A_i3.p2, not unique enough --skipping training candidate: Cnx99A_i4.p2, not unique enough +-skipping training candidate: Cnx99A_i2.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i4.p2, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough --skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i6.p4, not unique enough +-skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: ogre_i3.p2, not unique enough --skipping training candidate: CG6024_i2.p3, not unique enough --skipping training candidate: hrg_i1.p3, not unique enough +-skipping training candidate: CG6024_i1.p3, not unique enough -skipping training candidate: hrg_i3.p3, not unique enough +-skipping training candidate: hrg_i1.p3, not unique enough -skipping training candidate: ATPsyn-d_i3.p2, not unique enough +-skipping training candidate: CG6091_i1.p3, not unique enough -skipping training candidate: CG6091_i4.p3, not unique enough --skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough --skipping training candidate: CG33970_i3.p2, not unique enough -skipping training candidate: CG33970_i2.p2, not unique enough --skipping training candidate: eIF5B_i3.p5, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough --skipping training candidate: Aldh-III_i11.p2, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough +-skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i3.p2, not unique enough --skipping training candidate: CG13284_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i8.p2, not unique enough +-skipping training candidate: CG13284_i1.p2, not unique enough -skipping training candidate: CG13284_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_i3.p2, not unique enough -skipping training candidate: Lip4_i1.p2, not unique enough -skipping training candidate: Dgk_i7.p7, not unique enough --skipping training candidate: Dgk_i5.p4, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough --skipping training candidate: Dgk_i4.p4, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough +-skipping training candidate: Dgk_i2.p7, not unique enough +-skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Tm1_i16.p3, not unique enough -skipping training candidate: Tm1_i13.p3, not unique enough --skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: Tm1_i14.p3, not unique enough --skipping training candidate: CG8312_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough --skipping training candidate: CG8312_i3.p3, not unique enough --skipping training candidate: CG8312_i3.p4, not unique enough -skipping training candidate: CG8312_i2.p3, not unique enough -skipping training candidate: CG8312_i2.p4, not unique enough --skipping training candidate: Klp10A_i3.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: CG8312_i4.p3, not unique enough +-skipping training candidate: CG8312_i4.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_i4.p4, not unique enough +-skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough -skipping training candidate: Klp10A_i5.p4, not unique enough --skipping training candidate: eff_i3.p2, not unique enough -skipping training candidate: eff_i1.p2, not unique enough --skipping training candidate: CG14995_i4.p4, not unique enough +-skipping training candidate: eff_i3.p2, not unique enough -skipping training candidate: CG14995_i5.p5, not unique enough --skipping training candidate: CG14995_i7.p4, not unique enough +-skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i6.p4, not unique enough +-skipping training candidate: CG14995_i7.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough +-skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i4.p4, not unique enough -skipping training candidate: CG12581_i2.p3, not unique enough --skipping training candidate: CG32082_i2.p3, not unique enough +-skipping training candidate: CG32082_i1.p3, not unique enough -skipping training candidate: CG32082_i3.p3, not unique enough --skipping training candidate: CG32082_i4.p5, not unique enough --skipping training candidate: Cnx99A_i3.p3, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p3, not unique enough -skipping training candidate: Cnx99A_i1.p3, not unique enough +-skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Cdep_i2.p6, not unique enough --skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough --skipping training candidate: CG33970_i3.p3, not unique enough -skipping training candidate: CG33970_i2.p3, not unique enough +-skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: Sec16_i5.p6, not unique enough --skipping training candidate: Sec16_i2.p7, 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_i1.p7, not unique enough --skipping training candidate: Sec16_i6.p5, not unique enough +-skipping training candidate: Sec16_i2.p7, not unique enough -skipping training candidate: mge_i3.p1, not unique enough --skipping training candidate: CG6024_i2.p4, not unique enough --skipping training candidate: Myo61F_i3.p2, not unique enough --skipping training candidate: Myo61F_i4.p2, not unique enough +-skipping training candidate: CG6024_i1.p4, not unique enough -skipping training candidate: Myo61F_i1.p2, not unique enough +-skipping training candidate: Myo61F_i2.p2, not unique enough +-skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: 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: Cnx99A_i1.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_i2.p2, not unique enough --skipping training candidate: CG6145_i4.p2, not unique enough --skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG6145_i5.p2, 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_i5.p3, not unique enough +-skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG6145_i3.p2, not unique enough +-skipping training candidate: Calx_i2.p3, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough -skipping training candidate: Calx_i3.p3, not unique enough -skipping training candidate: Calx_i4.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_i8.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i2.p3, not unique enough --skipping training candidate: mge_i2.p2, not unique enough +-skipping training candidate: mge_i1.p2, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough -skipping training candidate: AdipoR_i4.p3, not unique enough --skipping training candidate: AdipoR_i5.p2, not unique enough --skipping training candidate: Aldh-III_i1.p2, not unique enough +-skipping training candidate: AdipoR_i3.p3, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough --skipping training candidate: Aldh-III_i9.p2, not unique enough --skipping training candidate: Cdep_i2.p9, not unique enough +-skipping training candidate: Aldh-III_i1.p2, not unique enough +-skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough --skipping training candidate: Cdep_i4.p3, not unique enough +-skipping training candidate: Cdep_i2.p9, not unique enough +-skipping training candidate: hrg_i3.p4, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough --skipping training candidate: hrg_i3.p4, not unique enough --skipping training candidate: CG33125_i2.p2, not unique enough +-skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i2.p4, not unique enough -skipping training candidate: Sec16_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough --skipping training candidate: Sec16_i2.p8, not unique enough --skipping training candidate: Sec16_i2.p9, not unique enough --skipping training candidate: Sec16_i4.p8, not unique enough --skipping training candidate: Sec16_i4.p9, not unique enough --skipping training candidate: Sec16_i1.p8, not unique enough --skipping training candidate: Sec16_i1.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_i3.p7, not unique enough +-skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i4.p8, not unique enough +-skipping training candidate: Sec16_i4.p9, not unique enough +-skipping training candidate: Sec16_i2.p8, not unique enough +-skipping training candidate: Sec16_i2.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_i4.p4, not unique enough --skipping training candidate: CG6091_i3.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough +-skipping training candidate: CG6091_i4.p4, not unique enough -skipping training candidate: CanB2_i2.p2, not unique enough -skipping training candidate: IP3K1_i1.p3, not unique enough --skipping training candidate: Klp10A_i3.p5, not unique enough --skipping training candidate: Klp10A_i2.p8, 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_i6.p5, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: Klp10A_i5.p5, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough --skipping training candidate: Cdep_i2.p10, not unique enough +-skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough --skipping training candidate: Cdep_i4.p4, not unique enough +-skipping training candidate: Cdep_i2.p10, not unique enough -skipping training candidate: Est-6_i2.p2, not unique enough --skipping training candidate: Klp10A_i3.p6, not unique enough --skipping training candidate: Klp10A_i2.p9, 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_i6.p6, not unique enough -skipping training candidate: Klp10A_i1.p7, not unique enough -skipping training candidate: Klp10A_i5.p6, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i3.p4, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i3.p5, not unique enough --skipping training candidate: Cnx99A_i4.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough --skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Cnx99A_i4.p3, not unique enough -skipping training candidate: Myo61F_i1.p3, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough --skipping training candidate: Myo61F_i4.p4, not unique enough +-skipping training candidate: Myo61F_i2.p3, not unique enough +-skipping training candidate: Myo61F_i4.p3, not unique enough -skipping training candidate: Myo61F_i1.p4, not unique enough +-skipping training candidate: Myo61F_i2.p4, not unique enough +-skipping training candidate: Myo61F_i4.p4, not unique enough -skipping training candidate: bic_i2.p2, not unique enough --skipping training candidate: CG10082_i1.p5, not unique enough --skipping training candidate: CG32082_i2.p4, not unique enough +-skipping training candidate: CG10082_i2.p3, not unique enough +-skipping training candidate: CG32082_i1.p4, not unique enough -skipping training candidate: CG32082_i3.p4, not unique enough --skipping training candidate: CG32082_i4.p6, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough -skipping training candidate: Eno_i5.p6, not unique enough --skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i6.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_i1.p6, not unique enough +-skipping training candidate: Eno_i6.p5, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough +-skipping training candidate: 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: Sec16_i1.p10, not unique enough -skipping training candidate: Dgk_i7.p8, not unique enough --skipping training candidate: Dgk_i5.p5, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough --skipping training candidate: Dgk_i4.p5, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough +-skipping training candidate: Dgk_i2.p8, not unique enough +-skipping training candidate: Dgk_i5.p5, not unique enough -skipping training candidate: Dgk_i1.p6, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: nmo_i6.p3, not unique enough --skipping training candidate: CG33970_i2.p5, not unique enough --skipping training candidate: sqd_i5.p3, not unique enough --skipping training candidate: Dgk_i6.p7, 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_i1.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_i1.p1, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough +-skipping training candidate: His4r_i1.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough -skipping training candidate: Hsc70-1_i1.p4, not unique enough --skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: hrg_i3.p5, not unique enough --skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: CG8136_i4.p2, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough --skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: CG8136_i2.p2, not unique enough +-skipping training candidate: CG8136_i3.p2, not unique enough -skipping training candidate: Myo61F_i1.p5, not unique enough --skipping training candidate: CG6091_i4.p5, not unique enough --skipping training candidate: CG6091_i3.p5, not unique enough +-skipping training candidate: Myo61F_i2.p5, not unique enough +-skipping training candidate: Myo61F_i4.p5, not unique enough -skipping training candidate: CG6091_i2.p4, 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_i1.p3, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough +-skipping training candidate: CG6091_i4.p5, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough --skipping training candidate: gukh_i2.p3, not unique enough --skipping training candidate: sqd_i5.p4, not unique enough --skipping training candidate: CG33125_i2.p3, not unique enough --skipping training candidate: gukh_i2.p4, not unique enough +-skipping training candidate: CG6145_i1.p3, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough +-skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: gukh_i1.p4, not unique enough +-skipping training candidate: sqd_i3.p3, not unique enough +-skipping training candidate: CG33125_i1.p4, not unique enough +-skipping training candidate: gukh_i1.p5, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Mon Jun 9 04:29:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:27:24 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 Jun 9 04:29:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:29:50 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 Jun 9 04:29:55 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 May 8 00:27:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 May 8 00:27:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Wed May 8 00:27:45 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 Jun 9 04:29:56 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 Jun 9 04:29:56 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 Jun 9 04:29:56 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 May 8 00:27:45 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 May 8 00:27:46 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 May 8 00:27:47 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/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 Jun 9 04:30:25 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 May 8 00:29:16 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Jun 9 04:30:33 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 May 8 00:29:35 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:30:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Wed May 8 00:29:37 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Jun 9 04:30:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Wed May 8 00:29:40 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 Jun 9 04:30:36 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 May 8 00:29:42 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 Jun 9 04:30:37 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 May 8 00:29:44 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: -1.38055452447959 instead of -3.67354139778402 --feature swap of score: -1.4382558759228 instead of -3.43778648632495 --feature swap of score: -1.62019109495048 instead of -2.94544399620627 --feature swap of score: -1.42575109166135 instead of -1.43450642288024 --feature swap of score: -0.593410679004587 instead of -1.10282885774721 --feature swap of score: 1.99983919368621 instead of -1.09462870941224 --feature swap of score: -0.475753415573571 instead of -1.01576745125075 --feature swap of score: 2.78869162515984 instead of -0.967173003187271 --feature swap of score: -0.553238195767743 instead of -1.05874591922829 --feature swap of score: 2.42618230600017 instead of -0.980403209396385 --feature swap of score: -0.16975988661678 instead of -0.841560696233594 --feature swap of score: 0.742949309364656 instead of -0.853000231071735 --feature swap of score: 1.77335318100434 instead of -1.20584324620961 --feature swap of score: 1.39824129129916 instead of -1.41242355471491 --feature swap of score: -0.672328104472974 instead of -1.05319872737304 --feature swap of score: 0.0385710463603451 instead of -0.923923977705539 --feature swap of score: -0.460938829920523 instead of -1.16459214556615 --feature swap of score: -0.417005779178844 instead of -0.482543319180851 --feature swap of score: 1.35139009235795 instead of -0.440983103699267 --feature swap of score: 3.16506339004864 instead of -0.749879815316204 --feature swap of score: 1.8202874558987 instead of -0.241803615303654 --feature swap of score: 2.02578118979438 instead of -0.240219009383498 --feature swap of score: 2.1332966986232 instead of -0.138501892643493 --feature swap of score: 0.391994857326213 instead of -0.312475310956153 --feature swap of score: 2.71335512114063 instead of -0.204427710480474 --feature swap of score: 0.0370450695271914 instead of -0.401374237853217 --feature swap of score: 1.49710351491856 instead of -0.657065690579906 --feature swap of score: 1.87926842806384 instead of -0.68208203325157 --feature swap of score: 3.22799306163313 instead of -0.953943329856444 --feature swap of score: 1.16976115564617 instead of -0.942296768283865 --feature swap of score: 1.70182905711357 instead of -1.11038693950783 --feature swap of score: 0.849633016957488 instead of -0.62634254324572 --feature swap of score: 0.828298546396583 instead of -0.500134066921073 --feature swap of score: 1.55383824325366 instead of -0.721995758730931 --feature swap of score: -0.560479668752244 instead of -0.915233993820182 --feature swap of score: 0.314085550239882 instead of -0.159112356358461 --feature swap of score: 0.172307208635974 instead of -0.268884622163647 --feature swap of score: 1.58209512899553 instead of -0.123639428100379 --feature swap of score: 0.628509128421092 instead of -0.159776802028513 --feature swap of score: 1.12513708501665 instead of -0.152625586413572 --feature swap of score: 0.866850102603228 instead of 0.00590616464341218 --feature swap of score: 1.09458690401884 instead of 0.274590391925809 --feature swap of score: 3.1064108029275 instead of 0.293823498257673 --feature swap of score: 1.48019283498595 instead of -0.0275679593709219 --feature swap of score: 0.962095673091104 instead of 0.162697766345468 --feature swap of score: 2.0472695108668 instead of 0.153254911117506 --feature swap of score: 1.74138415208099 instead of 0.243279110656252 --feature swap of score: 0.809412681099786 instead of 0.18843690599997 --feature swap of score: 7.32112708558934 instead of -0.0237067467718743 --feature swap of score: 0.610906348573909 instead of 0.459404459440528 --feature swap of score: 2.0101520385922 instead of -0.0650202667177897 --feature swap of score: 8.93032337546103 instead of -0.451841099081849 --feature swap of score: 0.186952775942888 instead of -0.426053152566827 --num feature swaps: 53 --removed 1 / 75 from PWM based on low scores -* [Mon Jun 9 04:30:37 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: -1.35997627374599 instead of -3.73335111013678 +-feature swap of score: -1.40993082733663 instead of -3.41217092567503 +-feature swap of score: -1.65496798954626 instead of -3.01372485751611 +-feature swap of score: -1.37245060403815 instead of -1.41592696534351 +-feature swap of score: -1.10399493585 instead of -1.17647597138862 +-feature swap of score: -0.529110230193421 instead of -0.962262624108788 +-feature swap of score: 2.05008202524076 instead of -0.986261354105089 +-feature swap of score: -0.532973664378839 instead of -0.939207088875166 +-feature swap of score: 2.78758492323008 instead of -0.727199645902795 +-feature swap of score: -0.407157335152862 instead of -0.912597816814847 +-feature swap of score: 2.52858683085347 instead of -1.02945690195359 +-feature swap of score: -0.566798297783006 instead of -1.28631221250082 +-feature swap of score: 0.55871587269262 instead of -0.923214178346002 +-feature swap of score: 1.67806608906097 instead of -0.833121652838625 +-feature swap of score: 1.3377704266478 instead of -0.946243459936398 +-feature swap of score: -0.561431745812803 instead of -0.76955552920498 +-feature swap of score: 0.206627819759918 instead of -0.951354327176333 +-feature swap of score: -0.490533704545909 instead of -1.24062818885765 +-feature swap of score: -0.273668475733364 instead of -0.769430719990882 +-feature swap of score: -0.719631567801287 instead of -2.54046377062321 +-feature swap of score: 0.849499056915233 instead of -0.742679135264196 +-feature swap of score: 3.38339854682171 instead of -0.585764048514651 +-feature swap of score: 1.97062767579691 instead of -0.580269073977089 +-feature swap of score: 0.295706691031534 instead of -0.381173876908215 +-feature swap of score: 2.4601279204268 instead of -0.0260033676985105 +-feature swap of score: 0.280478075056349 instead of -0.0629737374043899 +-feature swap of score: 1.93115275813202 instead of -0.311803699618237 +-feature swap of score: 0.743810388489858 instead of -0.358284503796811 +-feature swap of score: 1.18322278224677 instead of -0.367867007435597 +-feature swap of score: 0.792608295132749 instead of -0.565195585172942 +-feature swap of score: 3.12396078104938 instead of -0.571343059989165 +-feature swap of score: 0.0226447725855311 instead of -0.56674735263152 +-feature swap of score: 0.849436648051355 instead of -0.683728583734777 +-feature swap of score: 0.624415106379916 instead of -0.976020078388258 +-feature swap of score: 1.25163048958928 instead of -1.04071913361399 +-feature swap of score: 0.501758806008453 instead of -0.927730897560142 +-feature swap of score: 0.100675757681144 instead of -0.606288702853189 +-feature swap of score: 0.0720719823138575 instead of -0.78582434789196 +-feature swap of score: 0.375883284279289 instead of -0.626795941188706 +-feature swap of score: 0.743604615420521 instead of -0.639848111491699 +-feature swap of score: 2.23196231845911 instead of -0.330367875181694 +-feature swap of score: 0.32339968600847 instead of -0.0405387950985461 +-feature swap of score: 0.304534186897345 instead of 0.017012120185264 +-feature swap of score: 0.135316980609153 instead of 0.034292297958928 +-feature swap of score: 1.32717597411182 instead of -0.0545007097709372 +-feature swap of score: 1.26472174302509 instead of -0.335329781782477 +-feature swap of score: 1.14665138734024 instead of -0.0554834586425245 +-feature swap of score: 2.8941519855387 instead of -0.200960284856367 +-feature swap of score: 0.025652407137822 instead of -0.0375181314277411 +-feature swap of score: 0.385313568108584 instead of 0.278392774485727 +-feature swap of score: 0.796189856767029 instead of 0.099661368003949 +-feature swap of score: 2.52007052827615 instead of 0.322394328553187 +-feature swap of score: 0.405054053287273 instead of 0.309301408720898 +-feature swap of score: 0.933811086609378 instead of 0.519934387899231 +-feature swap of score: 7.23964072950235 instead of 0.428225860670284 +-feature swap of score: 1.95671744981156 instead of 0.622393545146566 +-feature swap of score: 3.90141396970794 instead of 0.393446187495083 +-feature swap of score: 8.68687946239067 instead of -0.0146485068526612 +-num feature swaps: 58 +* [Wed May 8 00:29:44 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 Jun 9 04:31:06 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 May 8 00:31:08 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 Jun 9 04:31:14 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 May 8 00:31:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon Jun 9 04:31:15 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 May 8 00:31:27 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 Jun 9 04:31:16 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Wed May 8 00:31:29 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 Jun 9 04:31:18 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 May 8 00:31:30 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: 15 -* [Mon Jun 9 04:31:19 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 Jun 9 04:31:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed +-number of revised start positions: 12 +* [Wed May 8 00:31:31 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 May 8 00:31:31 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 Jun 9 04:31:19 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/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 May 8 00:31:31 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 Jun 9 04:31:19 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/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 May 8 00:31:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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.* @@ -13629,8 +13669,8 @@ -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. @@ -13770,12 +13810,14 @@ 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/975252/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/975252/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/1499937 and its subdirectories -I: Current time: Mon Jun 9 04:31:39 -12 2025 -I: pbuilder-time-stamp: 1749486699 +I: removing directory /srv/workspace/pbuilder/975252 and its subdirectories +I: Current time: Wed May 8 00:32:10 +14 2024 +I: pbuilder-time-stamp: 1715077930