Diff of the two buildlogs: -- --- b1/build.log 2025-03-01 08:23:30.754169702 +0000 +++ b2/build.log 2025-03-01 08:33:28.751067263 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 28 19:53:41 -12 2025 -I: pbuilder-time-stamp: 1740815621 +I: Current time: Sat Apr 4 04:46:32 +14 2026 +I: pbuilder-time-stamp: 1775227592 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/889743/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/911970/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Apr 3 14:46 /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/911970/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/911970/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e9e61ee0708245beb49d87b66ca658a3' - 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='889743' - PS1='# ' - PS2='> ' + INVOCATION_ID=36f3c22ec3024440a3fd2b485cd297c3 + 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=911970 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.S3fsBl7M/pbuilderrc_DstJ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S3fsBl7M/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://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S3fsBl7M/pbuilderrc_CZHP --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S3fsBl7M/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://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/889743/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/911970/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -284,7 +316,7 @@ Get: 163 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 130 MB in 2s (66.3 MB/s) +Fetched 130 MB in 2s (67.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19802 files and directories currently installed.) @@ -838,8 +870,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Mar 1 07:56:08 UTC 2025. -Universal Time is now: Sat Mar 1 07:56:08 UTC 2025. +Local time is now: Fri Apr 3 14:47:27 UTC 2026. +Universal Time is now: Fri Apr 3 14:47:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14) ... @@ -989,7 +1021,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes +I: user script /srv/workspace/pbuilder/911970/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/911970/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 @@ -1011,7 +1047,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j20 test + make -j42 test make[2]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' @@ -1052,7 +1088,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Fri Feb 28 19:56:44 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 +* [Sat Apr 4 04:47:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -1104,13 +1140,13 @@ fi -Building a new DB, current time: 02/28/2025 19:56:44 +Building a new DB, current time: 04/04/2026 04:47:51 New DB name: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/mini_sprot.db.pep New DB title: mini_sprot.db.pep Sequence type: Protein Keep MBits: T Maximum file size: 3000000000B -Adding sequences from FASTA; added 240 sequences in 0.011838 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00747585 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1185,8 +1221,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.04 -# Mc/sec: 367.11 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1640.61 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1243,8 +1279,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 611.33 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1685.69 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1309,7 +1345,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 947.78 +# Mc/sec: 2174.45 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1369,8 +1405,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 415.11 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2059.62 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1430,8 +1466,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 336.70 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 808.39 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1481,8 +1517,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 299.38 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 677.79 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1547,7 +1583,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 317.37 +# Mc/sec: 2312.95 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1599,8 +1635,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 265.49 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 736.17 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1651,7 +1687,7 @@ 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: 827.17 +# Mc/sec: 2229.20 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1707,8 +1743,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 898.02 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2136.13 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1796,8 +1832,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 459.80 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1789.04 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1881,8 +1917,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 578.12 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2003.73 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1938,8 +1974,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 492.58 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1051.40 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1995,8 +2031,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 594.46 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1177.42 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2052,8 +2088,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1564.98 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2893.26 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2098,7 +2134,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1394.27 +# Mc/sec: 2363.44 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2150,8 +2186,8 @@ 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: 1831.24 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3228.66 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2195,8 +2231,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1306.91 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2194.69 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2257,7 +2293,7 @@ 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: 981.19 +# Mc/sec: 1676.53 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2308,7 +2344,7 @@ 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: 390.17 +# Mc/sec: 1407.02 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2420,8 +2456,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 473.61 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1259.28 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2467,8 +2503,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 671.82 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2275.30 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2534,8 +2570,8 @@ 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: 309.52 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2042.20 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2573,8 +2609,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1800.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4102.60 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2650,8 +2686,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 633.42 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1565.65 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2704,7 +2740,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1452.38 +# Mc/sec: 2618.89 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2788,8 +2824,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 308.66 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 594.51 // Query: DLH [M=217] Accession: PF01738.17 @@ -2837,7 +2873,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1489.41 +# Mc/sec: 3461.25 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2884,7 +2920,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1339.22 +# Mc/sec: 2183.73 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 696.13 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3256.81 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2977,7 +3013,7 @@ 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: 1808.65 +# Mc/sec: 3669.91 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3023,7 +3059,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 668.22 +# Mc/sec: 1450.87 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3061,7 +3097,7 @@ 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: 1720.91 +# Mc/sec: 3648.51 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3113,7 +3149,7 @@ 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: 927.20 +# Mc/sec: 1761.05 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3151,7 +3187,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 765.09 +# Mc/sec: 1766.22 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3189,7 +3225,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1702.41 +# Mc/sec: 3158.61 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3240,7 +3276,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1156.17 +# Mc/sec: 2522.14 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3277,8 +3313,8 @@ 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: 2617.10 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4183.86 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3338,8 +3374,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1402.18 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2554.08 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3384,7 +3420,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1473.60 +# Mc/sec: 2725.47 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3440,8 +3476,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1055.11 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2554.46 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3495,8 +3531,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 469.83 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1021.65 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3533,8 +3569,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1979.53 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3867.33 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3611,7 +3647,7 @@ 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: 1513.62 +# Mc/sec: 2722.48 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3675,8 +3711,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 430.19 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 883.52 // Query: FPP [M=866] Accession: PF05911.10 @@ -3726,8 +3762,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 992.76 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2319.57 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3779,8 +3815,8 @@ 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: 1324.69 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2512.15 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3903,8 +3939,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 363.68 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 744.75 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3943,7 +3979,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 876.40 +# Mc/sec: 1786.82 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4033,8 +4069,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 366.14 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 905.62 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4084,8 +4120,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 302.77 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 697.13 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4146,7 +4182,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 491.42 +# Mc/sec: 1696.12 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4250,8 +4286,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 452.73 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 867.03 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4298,8 +4334,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1348.17 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2454.95 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4373,8 +4409,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 610.74 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1618.12 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4444,8 +4480,8 @@ 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: 859.51 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2150.73 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4492,8 +4528,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 461.19 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1157.92 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4563,8 +4599,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 214.16 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 412.69 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4615,7 +4651,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1688.24 +# Mc/sec: 3427.37 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4665,8 +4701,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.04 -# Mc/sec: 133.04 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3616.51 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4705,7 +4741,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1204.89 +# Mc/sec: 2538.98 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4750,7 +4786,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1180.05 +# Mc/sec: 2266.29 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4802,7 +4838,7 @@ 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: 909.42 +# Mc/sec: 1787.52 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4884,8 +4920,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 592.19 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1359.72 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4985,8 +5021,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05 -# Mc/sec: 303.77 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1027.01 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5040,8 +5076,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 829.17 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1723.21 // Query: IBR [M=62] Accession: PF01485.20 @@ -5078,8 +5114,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 929.08 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1976.74 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5126,8 +5162,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 599.78 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1345.10 // Query: malic [M=182] Accession: PF00390.18 @@ -5165,8 +5201,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 330.52 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3746.68 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5203,8 +5239,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 490.02 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1548.84 // Query: MatE [M=161] Accession: PF01554.17 @@ -5288,8 +5324,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.06 -# Mc/sec: 76.87 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1675.59 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5327,7 +5363,7 @@ 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: 1775.30 +# Mc/sec: 3745.18 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5501,8 +5537,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07 -# Mc/sec: 138.77 +# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 +# Mc/sec: 278.41 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5544,8 +5580,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 686.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2492.50 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5601,8 +5637,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 477.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1476.88 // Query: MIP [M=227] Accession: PF00230.19 @@ -5652,8 +5688,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 451.28 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2935.90 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5705,8 +5741,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.22 -# Mc/sec: 16.73 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1766.09 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5796,8 +5832,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1133.04 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2510.74 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5834,8 +5870,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1420.20 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2284.30 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5872,8 +5908,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1820.13 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3749.31 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5926,7 +5962,7 @@ 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: 1667.08 +# Mc/sec: 3022.97 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5963,8 +5999,8 @@ 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: 2158.65 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 4379.65 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6084,8 +6120,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 594.66 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1240.17 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6135,8 +6171,8 @@ 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: 1786.20 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3162.78 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6206,8 +6242,8 @@ 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: 1268.49 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2418.38 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6259,8 +6295,8 @@ 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: 650.70 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1283.78 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6322,8 +6358,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 882.96 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1991.95 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6425,8 +6461,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 -# Mc/sec: 170.39 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 350.74 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6474,7 +6510,7 @@ 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: 1528.41 +# Mc/sec: 2427.75 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6525,7 +6561,7 @@ 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: 1078.67 +# Mc/sec: 1666.56 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6576,7 +6612,7 @@ 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: 1365.42 +# Mc/sec: 2532.57 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6627,7 +6663,7 @@ 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: 1950.85 +# Mc/sec: 3579.24 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6672,7 +6708,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1955.31 +# Mc/sec: 3438.02 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6719,7 +6755,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1133.77 +# Mc/sec: 1636.31 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6783,8 +6819,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 377.56 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 721.80 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6828,8 +6864,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1378.99 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2352.95 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6882,7 +6918,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 655.32 +# Mc/sec: 1224.64 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6926,8 +6962,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1091.15 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3655.85 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7027,8 +7063,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05 -# Mc/sec: 258.40 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 643.83 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7072,8 +7108,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 518.61 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 972.87 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7125,8 +7161,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 500.64 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2971.32 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7199,8 +7235,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.10 -# Mc/sec: 58.42 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 549.81 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7260,8 +7296,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1282.70 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2528.89 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7306,7 +7342,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1472.68 +# Mc/sec: 2818.38 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7359,7 +7395,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1523.18 +# Mc/sec: 2685.24 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7397,7 +7433,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2728.26 +# Mc/sec: 6312.38 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7439,8 +7475,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 2039.93 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3595.70 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7502,8 +7538,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 -# Mc/sec: 371.61 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 939.28 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7540,8 +7576,8 @@ 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: 1464.78 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3907.92 // Query: Usher [M=551] Accession: PF00577.19 @@ -7585,8 +7621,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1495.96 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3254.80 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7633,7 +7669,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 401.30 +# Mc/sec: 1002.70 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7678,7 +7714,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 555.74 +# Mc/sec: 1053.91 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7722,8 +7758,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.11 -# Mc/sec: 7.06 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1117.34 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7778,7 +7814,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 504.61 +# Mc/sec: 1237.92 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7816,8 +7852,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 391.10 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 821.39 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7869,7 +7905,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 453.39 +# Mc/sec: 1129.14 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7917,7 +7953,7 @@ 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: 891.49 +# Mc/sec: 1886.92 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7956,14 +7992,14 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 772.94 +# Mc/sec: 1587.29 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Fri Feb 28 19:56:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 19:56:48 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 +* [Sat Apr 4 04:47:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sat Apr 4 04:47:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: CUFF.60.1.p1, not unique enough -skipping training candidate: CUFF.26.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p3, not unique enough @@ -7990,39 +8026,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Fri Feb 28 19:56:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:47:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 37 -* [Fri Feb 28 19:56:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Fri Feb 28 19:56:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 19:56:50 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 +* [Sat Apr 4 04:47:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Sat Apr 4 04:47:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Sat Apr 4 04:47:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Fri Feb 28 19:56:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Feb 28 19:56:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Fri Feb 28 19:56:51 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 +* [Sat Apr 4 04:47:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Sat Apr 4 04:47:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Sat Apr 4 04:47:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 19:57:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:48:14 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Feb 28 19:57:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sat Apr 4 04:48:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Feb 28 19:57:41 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 +* [Sat Apr 4 04:48:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Feb 28 19:57:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sat Apr 4 04:48:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 19:57:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Sat Apr 4 04:48:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 19:57:46 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 +* [Sat Apr 4 04:48:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 -feature swap of score: 1.94858034627835 instead of -0.884029553505083 @@ -8032,33 +8068,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Fri Feb 28 19:57:46 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 +* [Sat Apr 4 04:48:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 19:58:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:48:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Feb 28 19:58:28 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 || : +* [Sat Apr 4 04:48:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 19:58:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Sat Apr 4 04:48:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Feb 28 19:58:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sat Apr 4 04:48:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 19:58:33 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 +* [Sat Apr 4 04:48:47 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 1 -* [Fri Feb 28 19:58:33 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Fri Feb 28 19:58:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed +* [Sat Apr 4 04:48:48 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Sat Apr 4 04:48:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Fri Feb 28 19:58:34 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 +* [Sat Apr 4 04:48:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Fri Feb 28 19:58:34 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 +* [Sat Apr 4 04:48:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* @@ -8150,7 +8186,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Fri Feb 28 19:58:34 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 +* [Sat Apr 4 04:48:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -8174,8 +8210,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Fri Feb 28 19:58:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 19:58:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:48:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sat Apr 4 04:48:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough @@ -8850,37 +8886,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Fri Feb 28 19:58:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:48:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 -* [Fri Feb 28 19:58:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores -* [Fri Feb 28 19:58:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 19:58:53 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/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 +* [Sat Apr 4 04:48:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores +* [Sat Apr 4 04:48:54 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Sat Apr 4 04:49:00 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Fri Feb 28 19:58:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Feb 28 19:58:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Fri Feb 28 19:58:54 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 +* [Sat Apr 4 04:49:00 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Sat Apr 4 04:49:00 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Sat Apr 4 04:49:01 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 19:59:53 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 +* [Sat Apr 4 04:49:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Feb 28 20:00:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sat Apr 4 04:49:38 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:00:07 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.feature.scores.roc +* [Sat Apr 4 04:49:40 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Feb 28 20:00:09 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.+.pwm || : +* [Sat Apr 4 04:49:41 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:00:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Sat Apr 4 04:49:41 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:00:11 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 +* [Sat Apr 4 04:49:42 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 @@ -8939,33 +8975,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Fri Feb 28 20:00:11 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 +* [Sat Apr 4 04:49:42 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:01:10 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 +* [Sat Apr 4 04:50:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Feb 28 20:01:23 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 || : +* [Sat Apr 4 04:50:15 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:01:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Sat Apr 4 04:50:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Feb 28 20:01:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sat Apr 4 04:50:17 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:01:28 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 +* [Sat Apr 4 04:50:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 83 -* [Fri Feb 28 20:01:28 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Fri Feb 28 20:01:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:18 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Sat Apr 4 04:50:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Fri Feb 28 20:01:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Fri Feb 28 20:01:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* @@ -9022,8 +9058,8 @@ CDS coords: 80, 427 -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). --Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. --Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. +-Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 112, 447 @@ -9058,7 +9094,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Fri Feb 28 20:01:31 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 +* [Sat Apr 4 04:50:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -9078,8 +9114,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Fri Feb 28 20:01:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 20:01:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sat Apr 4 04:50:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0_seq2.p1, not unique enough -skipping training candidate: comp992_c0_seq2.p1, not unique enough -skipping training candidate: comp718_c0_seq2.p1, not unique enough @@ -9117,37 +9153,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Fri Feb 28 20:01:41 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 +* [Sat Apr 4 04:50:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 -* [Fri Feb 28 20:01:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores -* [Fri Feb 28 20:01:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 20:01:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores +* [Sat Apr 4 04:50:25 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Sat Apr 4 04:50:30 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Fri Feb 28 20:01:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Feb 28 20:01:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Fri Feb 28 20:02:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:50:30 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Sat Apr 4 04:50:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Sat Apr 4 04:50:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:03:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sat Apr 4 04:50:59 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Feb 28 20:03:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sat Apr 4 04:51:06 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:03:47 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 +* [Sat Apr 4 04:51:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Feb 28 20:03:49 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 || : +* [Sat Apr 4 04:51:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:03:50 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 || : +* [Sat Apr 4 04:51:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:03:51 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 +* [Sat Apr 4 04:51:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 @@ -9253,33 +9289,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Fri Feb 28 20:03:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:51:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:04:53 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 +* [Sat Apr 4 04:51:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Feb 28 20:05:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Sat Apr 4 04:51:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:05:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Sat Apr 4 04:51:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Feb 28 20:05:08 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sat Apr 4 04:51:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:05:09 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 +* [Sat Apr 4 04:51:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 43 -* [Fri Feb 28 20:05:09 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Fri Feb 28 20:05:09 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 +* [Sat Apr 4 04:51:49 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Sat Apr 4 04:51:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Fri Feb 28 20:05:09 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 +* [Sat Apr 4 04:51:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Fri Feb 28 20:05:10 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/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 +* [Sat Apr 4 04:51:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* @@ -9296,9 +9332,7 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp1051_c1_seq1', - 'contig' => 'III', - 'orient' => '-', + 'gene_id' => '', 'trans_id' => '', 'coords' => [ [ @@ -9306,21 +9340,23 @@ '1644586' ] ], - 'gene_id' => '' + 'asmbl' => 'comp1051_c1_seq1', + 'orient' => '-', + 'contig' => 'III' }; + mid_pt: 808 + is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=83.26 + gene_length: 1616 TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + is_pseudogene: 0 asmbl_id: comp1051_c1_seq1 - gene_length: 1616 + gene_type: protein-coding classification: annotated_genes - mid_pt: 808 + num_exons: 1 source: transdecoder - gene_type: protein-coding - is_3prime_partial: 0 is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=83.26 strand: + - num_exons: 1 - is_pseudogene: 0 Model_feat_name: comp1051_c1_seq1.p1 gene_synonyms: mRNA_coords @@ -9338,9 +9374,11 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'asmbl' => 'comp1058_c0_seq1', 'orient' => '-', 'contig' => 'I', - 'asmbl' => 'comp1058_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 5095548, @@ -9350,24 +9388,22 @@ 5095142, '5095301' ] - ], - 'trans_id' => '', - 'gene_id' => '' + ] }; - com_name: ORF type:5prime_partial (+),score=32.57 - is_5prime_partial: 0 is_3prime_partial: 0 - is_pseudogene: 0 - Model_feat_name: comp1058_c0_seq1.p1 - strand: + - num_exons: 1 + mid_pt: 248 asmbl_id: comp1058_c0_seq1 + is_pseudogene: 0 TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - gene_type: protein-coding - source: transdecoder - mid_pt: 248 classification: annotated_genes + gene_type: protein-coding gene_length: 496 + com_name: ORF type:5prime_partial (+),score=32.57 + Model_feat_name: comp1058_c0_seq1.p1 + source: transdecoder + is_5prime_partial: 0 + num_exons: 1 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9390,7 +9426,10 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'orient' => '-', + 'contig' => 'III', + 'asmbl' => 'comp1112_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 2380416, @@ -9401,25 +9440,22 @@ '2380336' ] ], - 'trans_id' => '', - 'orient' => '-', - 'contig' => 'III', - 'asmbl' => 'comp1112_c0_seq1' + 'gene_id' => '' }; + mid_pt: 1041 + is_3prime_partial: 0 strand: + + is_5prime_partial: 0 + source: transdecoder num_exons: 1 - is_pseudogene: 0 Model_feat_name: comp1112_c0_seq1.p1 - is_3prime_partial: 0 - is_5prime_partial: 0 - com_name: ORF type:complete (+),score=155.28 gene_length: 2081 + com_name: ORF type:complete (+),score=155.28 classification: annotated_genes - mid_pt: 1041 - source: transdecoder gene_type: protein-coding - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + is_pseudogene: 0 asmbl_id: comp1112_c0_seq1 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9441,9 +9477,7 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', - 'asmbl' => 'comp1198_c0_seq1', - 'orient' => '-', + 'gene_id' => '', 'trans_id' => '', 'coords' => [ [ @@ -9463,22 +9497,24 @@ '401683' ] ], - 'gene_id' => '' + 'orient' => '-', + 'contig' => 'II', + 'asmbl' => 'comp1198_c0_seq1' }; - asmbl_id: comp1198_c0_seq1 - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 mid_pt: 299 - gene_type: protein-coding + is_3prime_partial: 0 + strand: + + num_exons: 1 source: transdecoder - classification: annotated_genes - gene_length: 597 is_5prime_partial: 0 - com_name: ORF type:internal (+),score=37.56 - is_3prime_partial: 0 Model_feat_name: comp1198_c0_seq1.p1 + com_name: ORF type:internal (+),score=37.56 + gene_length: 597 + gene_type: protein-coding + classification: annotated_genes + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 is_pseudogene: 0 - num_exons: 1 - strand: + + asmbl_id: comp1198_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9506,6 +9542,10 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'orient' => '-', + 'asmbl' => 'comp1210_c0_seq1', + 'contig' => 'III', 'trans_id' => '', 'coords' => [ [ @@ -9516,26 +9556,22 @@ 367430, '368790' ] - ], - 'asmbl' => 'comp1210_c0_seq1', - 'contig' => 'III', - 'orient' => '-', - 'gene_id' => '' + ] }; - Model_feat_name: comp1210_c0_seq1.p1 - is_pseudogene: 0 - num_exons: 1 - strand: + - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=12.16 is_3prime_partial: 0 mid_pt: 777 + Model_feat_name: comp1210_c0_seq1.p1 + strand: + source: transdecoder - gene_type: protein-coding - gene_length: 1554 + is_5prime_partial: 0 + num_exons: 1 classification: annotated_genes + gene_type: protein-coding + is_pseudogene: 0 asmbl_id: comp1210_c0_seq1 TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + gene_length: 1554 + com_name: ORF type:5prime_partial (+),score=12.16 gene_synonyms: mRNA_coords CDS_coords @@ -9560,32 +9596,32 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'trans_id' => '', + 'orient' => '-', + 'asmbl' => 'comp366_c0_seq1', + 'contig' => 'II', 'coords' => [ [ '3840968', '3841303' ] ], - 'contig' => 'II', - 'asmbl' => 'comp366_c0_seq1', - 'orient' => '-' + 'trans_id' => '', + 'gene_id' => '' }; - asmbl_id: comp366_c0_seq1 - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + is_3prime_partial: 0 mid_pt: 170 + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + asmbl_id: comp366_c0_seq1 + is_pseudogene: 0 gene_type: protein-coding - source: transdecoder classification: annotated_genes - gene_length: 340 - is_5prime_partial: 0 com_name: ORF type:internal (-),score=12.83 - is_3prime_partial: 0 - is_pseudogene: 0 + gene_length: 340 Model_feat_name: comp366_c0_seq1.p1 - strand: - num_exons: 1 + is_5prime_partial: 0 + source: transdecoder + strand: - gene_synonyms: mRNA_coords CDS_coords @@ -9611,9 +9647,6 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'asmbl' => 'comp610_c0_seq1', - 'contig' => 'I', 'coords' => [ [ '5471264', @@ -9621,22 +9654,25 @@ ] ], 'trans_id' => '', + 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp610_c0_seq1', 'gene_id' => '' }; mid_pt: 755 + is_3prime_partial: 0 + strand: + source: transdecoder - gene_type: protein-coding + is_5prime_partial: 0 + num_exons: 1 + Model_feat_name: comp610_c0_seq1.p1 gene_length: 1509 + com_name: ORF type:5prime_partial (+),score=50.55 classification: annotated_genes + gene_type: protein-coding asmbl_id: comp610_c0_seq1 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - Model_feat_name: comp610_c0_seq1.p1 is_pseudogene: 0 - num_exons: 1 - strand: + - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=50.55 - is_3prime_partial: 0 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9655,32 +9691,32 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], - 'trans_id' => '', - 'orient' => '-', - 'asmbl' => 'comp645_c0_seq1', 'contig' => 'I', - 'gene_id' => '' + 'orient' => '-', + 'asmbl' => 'comp645_c0_seq1' }; is_3prime_partial: 0 - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=273.35 - strand: + - num_exons: 1 - is_pseudogene: 0 - Model_feat_name: comp645_c0_seq1.p1 + mid_pt: 1827 TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 asmbl_id: comp645_c0_seq1 + is_pseudogene: 0 + gene_type: protein-coding classification: annotated_genes + com_name: ORF type:5prime_partial (+),score=273.35 gene_length: 3653 - mid_pt: 1827 - gene_type: protein-coding + Model_feat_name: comp645_c0_seq1.p1 + num_exons: 1 source: transdecoder + is_5prime_partial: 0 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9696,7 +9732,6 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'coords' => [ [ 380308, @@ -9708,24 +9743,25 @@ ] ], 'trans_id' => '', + 'asmbl' => 'comp688_c0_seq1', 'orient' => '+', 'contig' => 'II', - 'asmbl' => 'comp688_c0_seq1' + 'gene_id' => '' }; is_3prime_partial: 0 - com_name: ORF type:complete (+),score=172.54 + mid_pt: 1392 + Model_feat_name: comp688_c0_seq1.p1 + num_exons: 1 + source: transdecoder is_5prime_partial: 0 strand: + - num_exons: 1 - is_pseudogene: 0 - Model_feat_name: comp688_c0_seq1.p1 TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 asmbl_id: comp688_c0_seq1 - gene_length: 2784 - classification: annotated_genes - source: transdecoder + is_pseudogene: 0 gene_type: protein-coding - mid_pt: 1392 + classification: annotated_genes + com_name: ORF type:complete (+),score=172.54 + gene_length: 2784 gene_synonyms: mRNA_coords CDS_coords @@ -9750,6 +9786,7 @@ Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 3753910, @@ -9760,25 +9797,24 @@ '3755057' ] ], - 'trans_id' => '', 'orient' => '+', 'asmbl' => 'comp856_c0_seq1', 'contig' => 'II' }; - is_5prime_partial: 0 - com_name: ORF type:complete (+),score=71.94 is_3prime_partial: 0 - Model_feat_name: comp856_c0_seq1.p1 - is_pseudogene: 0 - num_exons: 1 - strand: + - asmbl_id: comp856_c0_seq1 - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 mid_pt: 785 - source: transdecoder + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + asmbl_id: comp856_c0_seq1 + is_pseudogene: 0 gene_type: protein-coding - gene_length: 1569 classification: annotated_genes + com_name: ORF type:complete (+),score=71.94 + gene_length: 1569 + Model_feat_name: comp856_c0_seq1.p1 + num_exons: 1 + source: transdecoder + is_5prime_partial: 0 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9798,6 +9834,8 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 3727877, @@ -9812,26 +9850,24 @@ '3727657' ] ], - 'trans_id' => '', 'orient' => '-', 'asmbl' => 'comp873_c0_seq2', - 'contig' => 'II', - 'gene_id' => '' + 'contig' => 'II' }; + Model_feat_name: comp873_c0_seq2.p1 + strand: + + num_exons: 1 + is_5prime_partial: 0 + source: transdecoder + gene_type: protein-coding + classification: annotated_genes TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 asmbl_id: comp873_c0_seq2 - classification: annotated_genes + is_pseudogene: 0 + com_name: ORF type:5prime_partial (+),score=8.59 gene_length: 1025 - gene_type: protein-coding - source: transdecoder - mid_pt: 513 is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=8.59 - is_5prime_partial: 0 - num_exons: 1 - strand: + - Model_feat_name: comp873_c0_seq2.p1 - is_pseudogene: 0 + mid_pt: 513 gene_synonyms: mRNA_coords CDS_coords @@ -9856,6 +9892,7 @@ Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 1268244, @@ -9866,25 +9903,24 @@ '1268172' ] ], - 'trans_id' => '', 'orient' => '-', - 'contig' => 'III', - 'asmbl' => 'comp888_c0_seq1' + 'asmbl' => 'comp888_c0_seq1', + 'contig' => 'III' }; mid_pt: 295 - gene_type: protein-coding + is_3prime_partial: 0 + strand: + + is_5prime_partial: 0 source: transdecoder - classification: annotated_genes + num_exons: 1 + Model_feat_name: comp888_c0_seq1.p1 gene_length: 589 + com_name: ORF type:5prime_partial (+),score=23.94 + classification: annotated_genes + gene_type: protein-coding asmbl_id: comp888_c0_seq1 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 is_pseudogene: 0 - Model_feat_name: comp888_c0_seq1.p1 - strand: + - num_exons: 1 - is_5prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=23.94 - is_3prime_partial: 0 + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9906,10 +9942,6 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', - 'asmbl' => 'comp940_c0_seq1', - 'orient' => '+', - 'trans_id' => '', 'coords' => [ [ 105641, @@ -9920,22 +9952,26 @@ '106404' ] ], + 'trans_id' => '', + 'asmbl' => 'comp940_c0_seq1', + 'orient' => '+', + 'contig' => 'III', 'gene_id' => '' }; - TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 - asmbl_id: comp940_c0_seq1 - classification: annotated_genes - gene_length: 2129 - gene_type: protein-coding - source: transdecoder - mid_pt: 1065 is_3prime_partial: 0 - com_name: ORF type:complete (+),score=94.37 - is_5prime_partial: 0 + mid_pt: 1065 + Model_feat_name: comp940_c0_seq1.p1 strand: + num_exons: 1 + source: transdecoder + is_5prime_partial: 0 + gene_type: protein-coding + classification: annotated_genes + TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + asmbl_id: comp940_c0_seq1 is_pseudogene: 0 - Model_feat_name: comp940_c0_seq1.p1 + com_name: ORF type:complete (+),score=94.37 + gene_length: 2129 gene_synonyms: mRNA_coords CDS_coords @@ -9955,10 +9991,7 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp983_c0_seq1', - 'contig' => 'I', - 'orient' => '-', - 'trans_id' => '', + 'gene_id' => '', 'coords' => [ [ 4100066, @@ -9969,22 +10002,25 @@ '4100014' ] ], - 'gene_id' => '' + 'trans_id' => '', + 'asmbl' => 'comp983_c0_seq1', + 'orient' => '-', + 'contig' => 'I' }; - Model_feat_name: comp983_c0_seq1.p1 + gene_length: 1870 + com_name: ORF type:5prime_partial (+),score=143.65 + asmbl_id: comp983_c0_seq1 is_pseudogene: 0 + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + classification: annotated_genes + gene_type: protein-coding + source: transdecoder + is_5prime_partial: 0 num_exons: 1 strand: + - com_name: ORF type:5prime_partial (+),score=143.65 - is_5prime_partial: 0 - is_3prime_partial: 0 - source: transdecoder - gene_type: protein-coding + Model_feat_name: comp983_c0_seq1.p1 mid_pt: 935 - gene_length: 1870 - classification: annotated_genes - asmbl_id: comp983_c0_seq1 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -10028,7 +10064,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Fri Feb 28 20:05:14 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 +* [Sat Apr 4 04:51:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -10053,8 +10089,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Fri Feb 28 20:05:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 20:05:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:52:03 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sat Apr 4 04:52:04 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: NM_198270.p1, not unique enough -skipping training candidate: NR_104391.p1, not unique enough -skipping training candidate: NR_104395.p1, not unique enough @@ -12672,37 +12708,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Fri Feb 28 20:06:04 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 +* [Sat Apr 4 04:52:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Fri Feb 28 20:06:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores -* [Fri Feb 28 20:06:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 20:08:55 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/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 +* [Sat Apr 4 04:52:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores +* [Sat Apr 4 04:52:10 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Sat Apr 4 04:52:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Fri Feb 28 20:09:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Feb 28 20:09:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Fri Feb 28 20:09:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:52:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Sat Apr 4 04:52:45 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Sat Apr 4 04:52:46 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:11:17 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:53:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Feb 28 20:11:42 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 || : +* [Sat Apr 4 04:53:28 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:11:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sat Apr 4 04:53:29 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Feb 28 20:11:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sat Apr 4 04:53:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:11:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Sat Apr 4 04:53:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:11:56 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 +* [Sat Apr 4 04:53:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 336 num_incorporate: 100 -feature swap of score: 3.78911079353454 instead of -4.15762669956 -feature swap of score: 4.3075564869904 instead of -3.54241712691985 @@ -12763,7 +12799,7 @@ -feature swap of score: 3.99301668862372 instead of 1.24561259795263 -feature swap of score: 1.72372236527001 instead of 1.02241527158741 -feature swap of score: 6.86300883201794 instead of 1.14563582053961 --feature swap of score: 5.54190533772704 instead of 1.28297492173033 +-feature swap of score: 5.54190533772704 instead of 1.28297492173032 -feature swap of score: 2.51308026289154 instead of 1.4180584754329 -feature swap of score: 3.38846514773249 instead of 1.2857641622143 -feature swap of score: 2.49385651598659 instead of 1.55130322997112 @@ -12805,33 +12841,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Fri Feb 28 20:11:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:53:33 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:14:43 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 +* [Sat Apr 4 04:54:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Feb 28 20:15:12 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 || : +* [Sat Apr 4 04:54:14 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:15:19 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 +* [Sat Apr 4 04:54:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Feb 28 20:15:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sat Apr 4 04:54:18 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:15:30 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 +* [Sat Apr 4 04:54:19 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 -* [Fri Feb 28 20:15:34 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Fri Feb 28 20:15:34 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 +* [Sat Apr 4 04:54:22 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Sat Apr 4 04:54:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Fri Feb 28 20:15:36 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 +* [Sat Apr 4 04:54:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Fri Feb 28 20:15:44 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 +* [Sat Apr 4 04:54:26 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* @@ -12943,7 +12979,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Fri Feb 28 20:16:29 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 +* [Sat Apr 4 04:54:35 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. @@ -12967,10 +13003,10 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Fri Feb 28 20:16:35 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/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Feb 28 20:16:36 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 +* [Sat Apr 4 04:54:37 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sat Apr 4 04:54:37 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: bdg_i4.p1, not unique enough +-skipping training candidate: bdg_i3.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 @@ -12978,32 +13014,32 @@ -skipping training candidate: eIF5B_i3.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough --skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: Dgk_i3.p1, not unique enough +-skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i3.p1, not unique enough +-skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough --skipping training candidate: Calx_i1.p1, not unique enough --skipping training candidate: Calx_i4.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_i1.p1, not unique enough -skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough --skipping training candidate: Klp10A_i5.p1, not unique enough --skipping training candidate: Klp10A_i2.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: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough +-skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough --skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough -skipping training candidate: CG33970_i2.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough @@ -13012,92 +13048,92 @@ -skipping training candidate: CG10082_i2.p1, not unique enough -skipping training candidate: CG12581_i2.p1, not unique enough -skipping training candidate: CG6091_i3.p1, not unique enough --skipping training candidate: hrg_i2.p1, not unique enough --skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: hrg_i4.p1, not unique enough +-skipping training candidate: hrg_i1.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_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p1, not unique enough +-skipping training candidate: Npl4_i1.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough -skipping training candidate: l(3)05822_i3.p1, not unique enough --skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i3.p1, not unique enough +-skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough --skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough +-skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough --skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough +-skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough --skipping training candidate: Est-6_i1.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: 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_i3.p1, not unique enough -skipping training candidate: Eno_i5.p1, not unique enough +-skipping training candidate: Eno_i1.p1, not unique enough -skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough +-skipping training candidate: Aldh-III_i3.p1, not unique enough +-skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_i6.p1, not unique enough -skipping training candidate: Aldh-III_i7.p1, not unique enough --skipping training candidate: Aldh-III_i4.p1, not unique enough --skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough -skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough --skipping training candidate: 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_i1.p2, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough -skipping training candidate: Eno_i5.p2, not unique enough --skipping training candidate: Eno_i4.p2, not unique enough +-skipping training candidate: Eno_i1.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough --skipping training candidate: CG6424_i3.p2, not unique enough --skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: CG6424_i1.p2, not unique enough +-skipping training candidate: CG6424_i4.p2, not unique enough +-skipping training candidate: CG6424_i3.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough --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_i5.p1, not unique enough -skipping training candidate: AdipoR_i3.p1, not unique enough +-skipping training candidate: AdipoR_i4.p1, not unique enough -skipping training candidate: 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: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough --skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i1.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough --skipping training candidate: CG8136_i1.p1, not unique enough +-skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough --skipping training candidate: CG7564_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_i5.p1, not unique enough -skipping training candidate: nmo_i4.p1, not unique enough +-skipping training candidate: nmo_i5.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough @@ -13107,557 +13143,558 @@ -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_i4.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_i1.p1, not unique enough +-skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i3.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough -skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough -skipping training candidate: CG13284_i3.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough --skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: CG13284_i2.p1, not unique enough +-skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough --skipping training candidate: Klp10A_i5.p2, not unique enough --skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Klp10A_i1.p2, not unique enough +-skipping training candidate: Klp10A_i5.p2, not unique enough -skipping training candidate: Klp10A_i3.p2, not unique enough -skipping training candidate: Klp10A_i4.p2, not unique enough +-skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough --skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough +-skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough -skipping training candidate: regucalcin_i2.p1, not unique enough --skipping training candidate: regucalcin_i4.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: l(3)05822_i2.p2, not unique enough +-skipping training candidate: l(3)05822_i3.p2, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough --skipping training candidate: l(3)05822_i4.p2, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Tm1_i9.p1, not unique enough --skipping training candidate: Tm1_i11.p1, not unique enough +-skipping training candidate: l(3)05822_i2.p2, not unique enough -skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Tm1_i11.p1, not unique enough +-skipping training candidate: Tm1_i9.p1, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough +-skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Npl4_i3.p2, not unique enough --skipping training candidate: Npl4_i2.p2, not unique enough +-skipping training candidate: Npl4_i1.p2, not unique enough +-skipping training candidate: Sec16_i2.p2, not unique enough -skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough --skipping training candidate: Sec16_i2.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough --skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i4.p2, not unique enough +-skipping training candidate: Dgk_i7.p2, not unique enough -skipping training candidate: eIF5B_i5.p2, not unique enough +-skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: eIF5B_i4.p2, not unique enough -skipping training candidate: eIF5B_i3.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_i3.p2, not unique enough +-skipping training candidate: Dgk_i6.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: l(1)G0193_i1.p2, not unique enough +-skipping training candidate: 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: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough --skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough -skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough --skipping training candidate: l(3)05822_i2.p3, not unique enough +-skipping training candidate: l(3)05822_i3.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough --skipping training candidate: l(3)05822_i4.p3, not unique enough +-skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i1.p2, not unique enough +-skipping training candidate: Sec16_i6.p2, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: Sec16_i2.p3, not unique enough --skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG13887_i2.p1, not unique enough --skipping training candidate: CG14995_i7.p2, not unique enough +-skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough --skipping training candidate: nmo_i5.p2, not unique enough +-skipping training candidate: nmo_i1.p2, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough +-skipping training candidate: nmo_i5.p2, not unique enough +-skipping training candidate: nmo_i3.p2, not unique enough -skipping training candidate: nmo_i6.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough -skipping training candidate: nmo_i2.p2, not unique enough --skipping training candidate: nmo_i3.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_i3.p2, not unique enough +-skipping training candidate: gukh_i4.p3, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough --skipping training candidate: RpL15_i1.p1, not unique enough +-skipping training candidate: RpL15_i2.p1, not unique enough +-skipping training candidate: RpL15_i3.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough --skipping training candidate: RpL15_i3.p1, not unique enough --skipping training candidate: RpL15_i2.p1, not unique enough +-skipping training candidate: RpL15_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p3, not unique enough --skipping training candidate: Npl4_i2.p3, not unique enough --skipping training candidate: trc_i2.p2, not unique enough --skipping training candidate: Hsc70-1_i1.p3, not unique enough +-skipping training candidate: Npl4_i1.p3, not unique enough +-skipping training candidate: trc_i1.p2, not unique enough -skipping training candidate: Hsc70-1_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_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough --skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG10237_i4.p2, not unique enough -skipping training candidate: CG10237_i5.p2, not unique enough --skipping training candidate: CG10237_i3.p2, not unique enough +-skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: CG10237_i1.p2, not unique enough --skipping training candidate: Eno_i1.p3, not unique enough -skipping training candidate: Eno_i3.p3, not unique enough -skipping training candidate: Eno_i5.p3, not unique enough --skipping training candidate: Eno_i4.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: Sec16_i3.p2, not unique enough +-skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough --skipping training candidate: CG14995_i3.p3, not unique enough +-skipping training candidate: Sec16_i1.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough +-skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough -skipping training candidate: gukh_i2.p2, not unique enough --skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough +-skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: CG10082_i1.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough +-skipping training candidate: CG14995_i6.p3, not unique enough +-skipping training candidate: CG30438_i2.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: CG30438_i3.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough -skipping training candidate: cdi_i2.p2, not unique enough +-skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i2.p1, not unique enough -skipping training candidate: ADD1_i2.p2, not unique enough --skipping training candidate: Sec16_i3.p3, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: bic_i2.p1, not unique enough +-skipping training candidate: Sec16_i1.p4, not unique enough +-skipping training candidate: bic_i1.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_i1.p1, not unique enough +-skipping training candidate: ctp_i4.p1, not unique enough -skipping training candidate: ctp_i3.p1, not unique enough --skipping training candidate: hrg_i3.p2, not unique enough +-skipping training candidate: ctp_i2.p1, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough --skipping training candidate: Eno_i1.p4, not unique enough +-skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: Eno_i3.p4, not unique enough -skipping training candidate: Eno_i5.p4, not unique enough --skipping training candidate: Eno_i4.p4, not unique enough +-skipping training candidate: Eno_i1.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Klp10A_i5.p3, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Eno_i4.p4, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough +-skipping training candidate: Klp10A_i5.p3, not unique enough -skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Calx_i5.p2, not unique enough -skipping training candidate: Calx_i3.p2, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough +-skipping training candidate: Calx_i6.p2, not unique enough +-skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i9.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_i8.p2, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough --skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough +-skipping training candidate: CG7564_i3.p3, not unique enough -skipping training candidate: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: eIF5B_i5.p3, not unique enough +-skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: eIF5B_i3.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_i3.p2, not unique enough --skipping training candidate: CG6424_i3.p3, not unique enough --skipping training candidate: CG6424_i2.p3, not unique enough +-skipping training candidate: AdipoR_i4.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: Tm1_i5.p2, not unique enough --skipping training candidate: Tm1_i14.p2, not unique enough +-skipping training candidate: CG6424_i4.p3, not unique enough +-skipping training candidate: CG6424_i3.p3, not unique enough +-skipping training candidate: CG6424_i3.p4, not unique enough -skipping training candidate: Tm1_i16.p2, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough +-skipping training candidate: Tm1_i14.p2, not unique enough +-skipping training candidate: Tm1_i13.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_i1.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: cdi_i2.p3, not unique enough -skipping training candidate: eff_i1.p1, not unique enough --skipping training candidate: eff_i2.p1, not unique enough +-skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i4.p5, not unique enough -skipping training candidate: eIF5B_i5.p4, not unique enough +-skipping training candidate: eIF5B_i2.p4, not unique enough +-skipping training candidate: eIF5B_i4.p5, not unique enough -skipping training candidate: eIF5B_i3.p4, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: Sec16_i4.p5, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i5.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_i2.p2, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough --skipping training candidate: CG3530_i3.p2, not unique enough +-skipping training candidate: CG32082_i3.p2, not unique enough -skipping training candidate: CG3530_i1.p2, not unique enough +-skipping training candidate: CG3530_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p6, not unique enough --skipping training candidate: l(3)05822_i2.p4, not unique enough +-skipping training candidate: l(3)05822_i3.p4, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough --skipping training candidate: l(3)05822_i4.p4, not unique enough --skipping training candidate: sqd_i2.p2, not unique enough --skipping training candidate: CG7564_i2.p6, not unique enough +-skipping training candidate: l(3)05822_i2.p4, not unique enough +-skipping training candidate: sqd_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: CG7564_i3.p4, not unique enough -skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough -skipping training candidate: cdi_i2.p4, not unique enough --skipping training candidate: CG6091_i2.p2, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: CG6091_i4.p2, not unique enough --skipping training candidate: Cdep_i1.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough +-skipping training candidate: Cdep_i1.p2, not unique enough +-skipping training candidate: Cnx99A_i4.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough --skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Cnx99A_i2.p2, not unique enough --skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: Sec16_i6.p4, not unique enough +-skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i5.p5, not unique enough -skipping training candidate: ogre_i3.p2, not unique enough -skipping training candidate: CG6024_i1.p3, not unique enough -skipping training candidate: hrg_i1.p3, not unique enough --skipping training candidate: hrg_i4.p3, not unique enough --skipping training candidate: ATPsyn-d_i1.p2, not unique enough +-skipping training candidate: hrg_i3.p3, not unique enough +-skipping training candidate: ATPsyn-d_i3.p2, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: CG6091_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough --skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: CG33970_i2.p2, not unique enough +-skipping training candidate: CG33970_i3.p2, not unique enough +-skipping training candidate: eIF5B_i1.p5, not unique enough -skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: eIF5B_i3.p5, 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: Aldh-III_i8.p2, not unique enough -skipping training candidate: CG13284_i5.p2, not unique enough +-skipping training candidate: CG13284_i1.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: CG13284_i2.p2, not unique enough --skipping training candidate: Lip4_i2.p2, not unique enough -skipping training candidate: Lip4_i1.p2, not unique enough +-skipping training candidate: Lip4_i3.p2, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i4.p4, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough --skipping training candidate: Tm1_i5.p3, not unique enough --skipping training candidate: Tm1_i14.p3, not unique enough -skipping training candidate: Tm1_i16.p3, not unique enough --skipping training candidate: CG8312_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough --skipping training candidate: CG8312_i2.p3, not unique enough --skipping training candidate: CG8312_i2.p4, not unique enough +-skipping training candidate: Tm1_i14.p3, not unique enough +-skipping training candidate: Tm1_i13.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: Klp10A_i5.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: CG8312_i2.p3, not unique enough +-skipping training candidate: CG8312_i2.p4, not unique enough +-skipping training candidate: CG8312_i1.p2, not unique enough +-skipping training candidate: CG8312_i1.p3, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough +-skipping training candidate: Klp10A_i5.p4, not unique enough -skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: Klp10A_i2.p6, not unique enough -skipping training candidate: eff_i1.p2, not unique enough --skipping training candidate: eff_i2.p2, not unique enough --skipping training candidate: CG14995_i3.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_i4.p4, not unique enough --skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG6424_i3.p5, not unique enough --skipping training candidate: CG6424_i2.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_i3.p4, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough +-skipping training candidate: CG6424_i4.p4, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough -skipping training candidate: CG12581_i2.p3, not unique enough --skipping training candidate: CG32082_i1.p3, not unique enough -skipping training candidate: CG32082_i2.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough --skipping training candidate: Cnx99A_i3.p3, not unique enough +-skipping training candidate: CG32082_i3.p3, not unique enough +-skipping training candidate: Cnx99A_i1.p3, not unique enough -skipping training candidate: Cnx99A_i2.p3, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough --skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: CG33970_i2.p3, not unique enough +-skipping training candidate: CG33970_i3.p3, not unique enough -skipping training candidate: Sec16_i3.p6, not unique enough --skipping training candidate: Sec16_i6.p5, not unique enough --skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, 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_i1.p7, not unique enough +-skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough -skipping training candidate: CG6024_i1.p4, not unique enough +-skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Myo61F_i2.p2, not unique enough -skipping training candidate: Myo61F_i1.p2, not unique enough --skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i3.p4, not unique enough +-skipping training candidate: Cnx99A_i1.p4, not unique enough -skipping training candidate: Cnx99A_i2.p4, not unique enough --skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG13887_i2.p2, not unique enough --skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG13887_i4.p2, not unique enough +-skipping training candidate: CG6145_i4.p2, not unique enough -skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG6145_i5.p2, not unique enough -skipping training candidate: CG6145_i1.p2, not unique enough --skipping training candidate: CG6145_i4.p2, not unique enough +-skipping training candidate: Calx_i5.p3, not unique enough -skipping training candidate: Calx_i3.p3, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough +-skipping training candidate: Calx_i6.p3, not unique enough +-skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i5.p3, not unique enough -skipping training candidate: Calx_i2.p3, not unique enough -skipping training candidate: Calx_i8.p3, not unique enough --skipping training candidate: mge_i1.p2, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough --skipping training candidate: AdipoR_i2.p2, not unique enough +-skipping training candidate: mge_i2.p2, not unique enough -skipping training candidate: AdipoR_i5.p2, not unique enough +-skipping training candidate: AdipoR_i1.p2, not unique enough -skipping training candidate: AdipoR_i3.p3, not unique enough --skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough --skipping training candidate: Aldh-III_i9.p2, not unique enough +-skipping training candidate: Aldh-III_i6.p2, not unique enough +-skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough --skipping training candidate: Cdep_i4.p3, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough +-skipping training candidate: Cdep_i1.p4, not unique enough -skipping training candidate: Cdep_i2.p9, not unique enough --skipping training candidate: hrg_i2.p2, not unique enough --skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i4.p4, not unique enough --skipping training candidate: CG33125_i2.p2, not unique enough +-skipping training candidate: hrg_i1.p4, not unique enough +-skipping training candidate: hrg_i3.p4, not unique enough +-skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i2.p4, not unique enough -skipping training candidate: Sec16_i3.p7, not unique enough -skipping training candidate: Sec16_i3.p8, not unique enough +-skipping training candidate: Sec16_i4.p8, not unique enough +-skipping training candidate: Sec16_i4.p9, not unique enough -skipping training candidate: Sec16_i6.p6, not unique enough -skipping training candidate: Sec16_i6.p7, not unique enough +-skipping training candidate: Sec16_i1.p8, not unique enough +-skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Sec16_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough --skipping training candidate: Sec16_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_i2.p3, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i3.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_i5.p5, not unique enough --skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough +-skipping training candidate: Klp10A_i5.p5, not unique enough -skipping training candidate: Klp10A_i3.p5, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough +-skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough --skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough +-skipping training candidate: Cdep_i1.p5, not unique enough -skipping training candidate: Cdep_i2.p10, not unique enough --skipping training candidate: Est-6_i1.p2, not unique enough --skipping training candidate: Klp10A_i5.p6, not unique enough --skipping training candidate: Klp10A_i2.p9, not unique enough +-skipping training candidate: Est-6_i2.p2, not unique enough -skipping training candidate: Klp10A_i1.p7, not unique enough +-skipping training candidate: Klp10A_i5.p6, not unique enough -skipping training candidate: Klp10A_i3.p6, not unique enough -skipping training candidate: Klp10A_i4.p6, not unique enough +-skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough +-skipping training candidate: Cnx99A_i4.p3, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough --skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Cnx99A_i2.p5, not unique enough +-skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough -skipping training candidate: Myo61F_i1.p3, not unique enough --skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough -skipping training candidate: Myo61F_i1.p4, not unique enough --skipping training candidate: Myo61F_i4.p4, not unique enough --skipping training candidate: bic_i2.p2, not unique enough +-skipping training candidate: bic_i1.p3, not unique enough -skipping training candidate: CG10082_i1.p5, not unique enough --skipping training candidate: CG32082_i1.p4, not unique enough -skipping training candidate: CG32082_i2.p4, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: Eno_i1.p6, not unique enough +-skipping training candidate: CG32082_i3.p4, not unique enough -skipping training candidate: Eno_i3.p5, not unique enough -skipping training candidate: Eno_i5.p6, not unique enough --skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: Eno_i1.p6, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough --skipping training candidate: Sec16_i1.p10, not unique enough +-skipping training candidate: Eno_i4.p6, not unique enough -skipping training candidate: Sec16_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_i1.p6, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough -skipping training candidate: Dgk_i5.p5, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough --skipping training candidate: Dgk_i4.p5, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i2.p8, not unique enough -skipping training candidate: nmo_i6.p3, not unique enough -skipping training candidate: CG33970_i2.p5, not unique enough -skipping training candidate: sqd_i3.p2, not unique enough -skipping training candidate: Dgk_i3.p7, not unique enough --skipping training candidate: Dgk_i1.p7, not unique enough --skipping training candidate: His4r_i2.p1, not unique enough +-skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: His4r_i3.p1, not unique enough --skipping training candidate: Hsc70-1_i1.p4, not unique enough +-skipping training candidate: His4r_i1.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: hrg_i1.p5, not unique enough --skipping training candidate: hrg_i4.p6, not unique enough --skipping training candidate: CG8136_i2.p2, not unique enough --skipping training candidate: CG8136_i3.p2, not unique enough +-skipping training candidate: hrg_i3.p5, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough +-skipping training candidate: CG8136_i2.p2, not unique enough +-skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough -skipping training candidate: Myo61F_i1.p5, not unique enough --skipping training candidate: Myo61F_i4.p5, not unique enough --skipping training candidate: CG6091_i2.p4, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i3.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: CG6145_i4.p3, not unique enough -skipping training candidate: CG6145_i2.p3, not unique enough +-skipping training candidate: CG6145_i5.p3, not unique enough -skipping training candidate: CG6145_i1.p3, not unique enough --skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: gukh_i2.p3, not unique enough -skipping training candidate: sqd_i3.p3, not unique enough --skipping training candidate: CG33125_i2.p3, not unique enough +-skipping training candidate: CG33125_i1.p4, not unique enough -skipping training candidate: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Fri Feb 28 20:16:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:54:37 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 49.4 -* [Fri Feb 28 20:16:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Fri Feb 28 20:16:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Fri Feb 28 20:17:06 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 +* [Sat Apr 4 04:54:37 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores +* [Sat Apr 4 04:54:38 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores +* [Sat Apr 4 04:54:43 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs -* [Fri Feb 28 20:17:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Feb 28 20:17:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Fri Feb 28 20:17:08 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 +* [Sat Apr 4 04:54:43 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement +Training start codon pattern recognition* [Sat Apr 4 04:54:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 +* [Sat Apr 4 04:54:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:18:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:55:13 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Feb 28 20:18:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sat Apr 4 04:55:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:19:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sat Apr 4 04:55:21 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Feb 28 20:19:08 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sat Apr 4 04:55:22 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:19:12 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 || : +* [Sat Apr 4 04:55:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:19:15 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 +* [Sat Apr 4 04:55:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 253 num_incorporate: 75 --feature swap of score: -1.32995414851447 instead of -3.68211301858989 --feature swap of score: -1.40028513755878 instead of -3.37710260527546 --feature swap of score: -1.69258413347498 instead of -3.01779709237978 --feature swap of score: -1.36298150899542 instead of -1.45631934879695 --feature swap of score: -1.09179095455133 instead of -1.23596899657769 --feature swap of score: -0.570290601331609 instead of -0.995909629525774 --feature swap of score: 2.07686517514861 instead of -0.969370133445289 --feature swap of score: -0.535239337227897 instead of -0.991225145210166 --feature swap of score: 2.82295090914258 instead of -0.746213479424158 --feature swap of score: -0.724807808055115 instead of -2.1682328457621 --feature swap of score: 2.17126450301995 instead of -1.07396602262494 --feature swap of score: -0.760629747084131 instead of -1.13531052291878 --feature swap of score: 0.192052006867624 instead of -1.34201276494794 --feature swap of score: 1.07549331083902 instead of -0.877385609866945 --feature swap of score: 1.843872466298 instead of -1.02720572361972 --feature swap of score: -1.08158944799666 instead of -1.26632293755379 --feature swap of score: 0.401248064087829 instead of -1.35333222247107 --feature swap of score: -0.407573250155134 instead of -1.39484052056645 --feature swap of score: -0.0637956069158349 instead of -1.09012640220857 --feature swap of score: 0.128902778418615 instead of -0.765641754480939 --feature swap of score: 1.02798315882703 instead of -0.368941821287104 --feature swap of score: 3.38696770471005 instead of -0.445423627061099 --feature swap of score: 1.8639344997537 instead of -0.752588479223261 --feature swap of score: 0.284612267600109 instead of -0.40001183612634 --feature swap of score: 2.63098126216197 instead of -0.465298126415992 --feature swap of score: 0.0501390309849949 instead of -0.59583226984869 --feature swap of score: -0.29789120625553 instead of -0.47489210082815 --feature swap of score: 1.13243415901331 instead of -0.220410467702445 --feature swap of score: 1.75856659741529 instead of -0.264199875003877 --feature swap of score: 0.328124136137351 instead of -0.0554217693832569 --feature swap of score: 2.01898809429988 instead of -0.251465367089326 --feature swap of score: 0.101373368351713 instead of -0.186190779656282 --feature swap of score: 0.245740279218803 instead of -0.228665012583865 --feature swap of score: -0.264956176744261 instead of -0.278419004176916 --feature swap of score: -0.0118727755765512 instead of -0.562922736982228 --feature swap of score: 1.69755603119932 instead of -0.49917214826656 --feature swap of score: 0.602303453392989 instead of -0.392363796394987 --feature swap of score: 2.25784525544873 instead of -0.603427852266763 --feature swap of score: 0.298048207853678 instead of 0.0129618616707136 --feature swap of score: 1.85106690896111 instead of -0.0772901470824624 --feature swap of score: 0.388206861542376 instead of 0.00524763943220263 --feature swap of score: 1.80023568458365 instead of 0.078165324169291 --feature swap of score: 0.601760443526604 instead of -1.35823799617647 --feature swap of score: 0.102391646628595 instead of -0.331816668925578 --feature swap of score: 2.07587230660837 instead of 0.148589128207844 --feature swap of score: 1.21989636243085 instead of 0.0587455011838274 --feature swap of score: 0.399804873641196 instead of -0.00436684154125219 --feature swap of score: 3.82244723647779 instead of 0.131399511096685 --feature swap of score: 1.60388404847681 instead of 0.0388278541105291 --feature swap of score: 3.23739167229734 instead of -0.555761182462342 --feature swap of score: 1.66234573013587 instead of 0.0998985862230385 --feature swap of score: 2.51966918907601 instead of 0.342432673352931 --feature swap of score: 4.83860772181895 instead of 0.181219904026928 --feature swap of score: 0.980633881146351 instead of 0.293135771661796 --feature swap of score: 5.85058103111519 instead of 0.386662929994367 --feature swap of score: 3.11916664938152 instead of 0.578346714502012 --num feature swaps: 56 -* [Fri Feb 28 20:19:16 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: -1.34957793453505 instead of -3.65904068288991 +-feature swap of score: -1.39572906560443 instead of -3.35216376315573 +-feature swap of score: -1.69630325759039 instead of -2.98117339663303 +-feature swap of score: -1.43768267123529 instead of -1.46708911321284 +-feature swap of score: -1.07366828356132 instead of -1.17169985727925 +-feature swap of score: -0.608644337531602 instead of -0.990961629190788 +-feature swap of score: 2.05001471772781 instead of -1.01844188447946 +-feature swap of score: -0.566166772692336 instead of -0.947586109976948 +-feature swap of score: 2.84340071546733 instead of -0.749932603539571 +-feature swap of score: -0.699947862815969 instead of -2.17195196987752 +-feature swap of score: 2.16755163647576 instead of -1.06617955835281 +-feature swap of score: -0.692363480155264 instead of -1.13141477923933 +-feature swap of score: 0.191620279280247 instead of -1.33745669299358 +-feature swap of score: 1.09322034204152 instead of -0.921715678531603 +-feature swap of score: 1.85175221534895 instead of -1.08829116479553 +-feature swap of score: -1.03936276354886 instead of -1.20229553050138 +-feature swap of score: 0.0244747088110545 instead of -1.26783961508813 +-feature swap of score: -0.199981782037446 instead of -1.14527871011785 +-feature swap of score: -0.0647550738316912 instead of -1.08648114988801 +-feature swap of score: 0.127050261849557 instead of -0.74127362528512 +-feature swap of score: 0.961626935343531 instead of -0.410337316808533 +-feature swap of score: 3.35786831737986 instead of -0.418375502827737 +-feature swap of score: 1.8822897091732 instead of -0.684322212294394 +-feature swap of score: 0.314289836900005 instead of -0.35832097248631 +-feature swap of score: 2.5857743233555 instead of -0.416998419549051 +-feature swap of score: 0.0188006437984154 instead of -0.554226899909981 +-feature swap of score: -0.272758880569481 instead of -0.429890551591147 +-feature swap of score: -0.206280156788655 instead of -0.237022826135258 +-feature swap of score: 1.18690256212264 instead of -0.143343806627715 +-feature swap of score: 1.43083845439511 instead of -0.0997072323959765 +-feature swap of score: -0.241916785025929 instead of -0.340034036557728 +-feature swap of score: 0.423895688999115 instead of -0.360910980427681 +-feature swap of score: 2.08402497787391 instead of -0.322583913217627 +-feature swap of score: 0.683172621280742 instead of -0.229180992557807 +-feature swap of score: 0.598667560844434 instead of -0.127968587427507 +-feature swap of score: -0.164146047680016 instead of -0.32910380970711 +-feature swap of score: -0.0839368493563616 instead of -0.568280974808266 +-feature swap of score: 1.26777651143307 instead of -0.238974394018944 +-feature swap of score: 0.969127502494966 instead of -0.184284062908186 +-feature swap of score: 1.69516641725281 instead of -0.0601674647771435 +-feature swap of score: 0.0920204564354837 instead of -0.145127494184619 +-feature swap of score: 1.96141444461694 instead of -0.1544353380988 +-feature swap of score: 0.716297533653149 instead of 0.191553216834918 +-feature swap of score: 0.136637180207062 instead of -1.2922896014903 +-feature swap of score: 2.2979061407518 instead of 0.151159711480821 +-feature swap of score: 1.64566121566819 instead of 0.248905026240191 +-feature swap of score: 0.842270225002328 instead of 0.296623514278357 +-feature swap of score: 0.00496914078554134 instead of -0.0326697985878739 +-feature swap of score: 3.29121307584141 instead of 0.186514040494963 +-feature swap of score: 1.54878195367595 instead of -0.16875278836663 +-feature swap of score: 3.40114977414137 instead of -0.0756315122158753 +-feature swap of score: 1.38449866072924 instead of 0.0269722043614823 +-feature swap of score: 2.32739236194744 instead of 0.637700107202835 +-feature swap of score: 4.50948309041247 instead of 0.591856922326118 +-feature swap of score: 1.06880731916353 instead of 0.401212009501844 +-feature swap of score: 5.77726236392425 instead of 0.647133541170604 +-feature swap of score: 3.42552043912303 instead of 0.603954740587356 +-num feature swaps: 57 +* [Sat Apr 4 04:55:23 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Feb 28 20:21:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sat Apr 4 04:55:56 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Feb 28 20:22:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Sat Apr 4 04:56:04 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Feb 28 20:22:15 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 +* [Sat Apr 4 04:56:06 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Feb 28 20:22:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sat Apr 4 04:56:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Feb 28 20:22:25 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 +* [Sat Apr 4 04:56:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. --number of revised start positions: 14 -* [Fri Feb 28 20:22:26 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Fri Feb 28 20:22:27 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/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: 13 +* [Sat Apr 4 04:56:08 2026] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Sat Apr 4 04:56:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Fri Feb 28 20:22:27 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/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 +* [Sat Apr 4 04:56:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep -* [Fri Feb 28 20:22:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds +* [Sat Apr 4 04:56:08 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* @@ -13807,8 +13844,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-deb: building package 'transdecoder' in '../transdecoder_5.7.1-2_all.deb'. +dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../transdecoder_5.7.1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../transdecoder_5.7.1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13816,12 +13853,14 @@ 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/911970/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/911970/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/889743 and its subdirectories -I: Current time: Fri Feb 28 20:23:29 -12 2025 -I: pbuilder-time-stamp: 1740817409 +I: removing directory /srv/workspace/pbuilder/911970 and its subdirectories +I: Current time: Sat Apr 4 04:56:27 +14 2026 +I: pbuilder-time-stamp: 1775228187