Diff of the two buildlogs: -- --- b1/build.log 2025-08-19 06:29:23.805714199 +0000 +++ b2/build.log 2025-08-19 06:45:40.394900899 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 18 18:21:14 -12 2025 -I: pbuilder-time-stamp: 1755584474 +I: Current time: Tue Sep 22 02:52:26 +14 2026 +I: pbuilder-time-stamp: 1789995146 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4072441/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/728110/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 21 12:52 /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/728110/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/728110/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c7c2e24e4ec34e6b9b1ad51cd3878a37' - 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='4072441' - PS1='# ' - PS2='> ' + INVOCATION_ID=7fca9debcda2465982944e6047d72dab + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=728110 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.10L0W10P/pbuilderrc_MoAr --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.10L0W10P/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.10L0W10P/pbuilderrc_B7jm --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.10L0W10P/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4072441/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/728110/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -85,7 +117,7 @@ Depends: debhelper-compat (= 13), liburi-perl, ncbi-blast+, hmmer, r-base-core, r-cran-ggplot2, r-bioc-seqlogo dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 20004 files and directories currently installed.) +(Reading database ... 20009 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -287,10 +319,10 @@ Get: 165 http://deb.debian.org/debian forky/main arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [425 kB] Get: 166 http://deb.debian.org/debian forky/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 128 MB in 1s (208 MB/s) +Fetched 128 MB in 1s (105 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20004 files and directories currently installed.) +(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 ... 20009 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:arm64. @@ -303,7 +335,7 @@ Setting up libexpat1:arm64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.6-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20338 files and directories currently installed.) +(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 ... 20343 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_arm64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. @@ -339,7 +371,7 @@ Unpacking libpython3-stdlib:arm64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. -(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 ... 21353 files and directories currently installed.) +(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 ... 21358 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_arm64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package libproc2-0:arm64. @@ -847,8 +879,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Aug 19 06:21:43 UTC 2025. -Universal Time is now: Tue Aug 19 06:21:43 UTC 2025. +Local time is now: Mon Sep 21 12:53:05 UTC 2026. +Universal Time is now: Mon Sep 21 12:53:05 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-15) ... @@ -1000,7 +1032,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes +I: user script /srv/workspace/pbuilder/728110/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/728110/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 @@ -1063,7 +1099,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Mon Aug 18 18:22:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue Sep 22 02:53:28 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. @@ -1115,13 +1151,13 @@ fi -Building a new DB, current time: 08/18/2025 18:22:00 +Building a new DB, current time: 09/22/2026 02:53:29 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 0.007761 seconds. +Adding sequences from FASTA; added 240 sequences in 0.00759888 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1197,7 +1233,7 @@ 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: 1843.76 +# Mc/sec: 1931.07 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1254,8 +1290,8 @@ 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: 1083.00 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1823.49 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1320,7 +1356,7 @@ 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: 1218.78 +# Mc/sec: 2246.12 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1381,7 +1417,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1309.75 +# Mc/sec: 2300.31 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1441,8 +1477,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 369.56 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 841.19 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1493,7 +1529,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 657.43 +# Mc/sec: 708.19 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1558,7 +1594,7 @@ 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: 1804.66 +# Mc/sec: 2477.01 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1611,7 +1647,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 722.86 +# Mc/sec: 767.17 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1661,8 +1697,8 @@ 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: 975.63 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2320.09 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1718,8 +1754,8 @@ 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: 1255.98 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2402.07 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1807,8 +1843,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 950.55 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1764.16 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1892,8 +1928,8 @@ 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: 818.24 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2051.89 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1949,8 +1985,8 @@ 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: 566.88 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1176.45 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -2006,8 +2042,8 @@ 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: 725.79 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1213.71 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2063,8 +2099,8 @@ 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: 2458.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3280.82 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2108,8 +2144,8 @@ 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: 1398.26 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2746.53 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2162,7 +2198,7 @@ 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: 2170.62 +# Mc/sec: 3486.16 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2206,8 +2242,8 @@ 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: 887.29 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2321.70 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2268,7 +2304,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1211.56 +# Mc/sec: 1773.26 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2318,8 +2354,8 @@ 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: 900.58 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1585.08 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2431,8 +2467,8 @@ 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: 1211.16 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1319.23 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2479,7 +2515,7 @@ 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: 1222.07 +# Mc/sec: 2668.38 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2546,7 +2582,7 @@ 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: 1487.96 +# Mc/sec: 545.10 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2584,8 +2620,8 @@ 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: 3548.33 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 4467.36 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2661,8 +2697,8 @@ 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: 1066.39 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1765.89 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2714,8 +2750,8 @@ 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: 1380.23 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2687.56 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2799,8 +2835,8 @@ 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: 451.04 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 279.18 // Query: DLH [M=217] Accession: PF01738.17 @@ -2847,8 +2883,8 @@ 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: 2646.53 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1363.12 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2895,7 +2931,7 @@ 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: 1146.80 +# Mc/sec: 585.81 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2945,7 +2981,7 @@ 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: 1860.18 +# Mc/sec: 895.29 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2988,7 +3024,7 @@ 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: 1722.68 +# Mc/sec: 649.61 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3033,8 +3069,8 @@ 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: 1165.12 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 730.41 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3071,8 +3107,8 @@ 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: 3002.94 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1858.86 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3124,7 +3160,7 @@ 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: 1295.78 +# Mc/sec: 342.32 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3161,8 +3197,8 @@ 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: 1119.10 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 347.99 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3200,7 +3236,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2107.97 +# Mc/sec: 715.78 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3250,8 +3286,8 @@ 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: 1142.09 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 683.77 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3288,8 +3324,8 @@ 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: 1950.53 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1366.02 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3350,7 +3386,7 @@ 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: 1054.41 +# Mc/sec: 845.22 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3395,7 +3431,7 @@ 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: 2529.60 +# Mc/sec: 1164.64 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3451,8 +3487,8 @@ 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: 2227.26 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1136.38 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3506,8 +3542,8 @@ 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: 1029.59 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 525.37 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3545,7 +3581,7 @@ 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: 1864.44 +# Mc/sec: 1101.46 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3621,8 +3657,8 @@ 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: 1465.23 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 780.18 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3686,8 +3722,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 426.38 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 306.84 // Query: FPP [M=866] Accession: PF05911.10 @@ -3737,8 +3773,8 @@ 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: 1517.60 +# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 1295.24 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3791,7 +3827,7 @@ 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: 1406.42 +# Mc/sec: 421.56 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3914,8 +3950,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 487.62 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 +# Mc/sec: 379.57 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3953,8 +3989,8 @@ 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: 1120.05 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 644.56 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4044,8 +4080,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 366.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03 +# Mc/sec: 414.53 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4095,8 +4131,8 @@ 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: 468.49 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 669.64 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4157,7 +4193,7 @@ 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: 706.17 +# Mc/sec: 1651.85 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4262,7 +4298,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 411.91 +# Mc/sec: 957.80 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4309,8 +4345,8 @@ 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: 1327.46 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2704.62 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4384,8 +4420,8 @@ 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: 722.98 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1610.07 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4456,7 +4492,7 @@ 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: 924.33 +# Mc/sec: 2314.43 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4503,8 +4539,8 @@ 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: 447.06 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1255.29 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4574,8 +4610,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 178.47 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 420.51 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4625,8 +4661,8 @@ 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: 1408.65 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3421.15 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4677,7 +4713,7 @@ 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: 2827.06 +# Mc/sec: 1169.19 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4715,8 +4751,8 @@ 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: 1921.37 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 757.67 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4761,7 +4797,7 @@ 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: 1784.37 +# Mc/sec: 512.63 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4813,7 +4849,7 @@ 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: 966.34 +# Mc/sec: 384.02 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4895,8 +4931,8 @@ 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: 1125.96 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 678.40 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4996,8 +5032,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 421.35 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03 +# Mc/sec: 426.39 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5051,8 +5087,8 @@ 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: 892.57 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 821.33 // Query: IBR [M=62] Accession: PF01485.20 @@ -5090,7 +5126,7 @@ 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: 2074.87 +# Mc/sec: 339.69 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5137,8 +5173,8 @@ 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: 1341.75 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 671.31 // Query: malic [M=182] Accession: PF00390.18 @@ -5177,7 +5213,7 @@ 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: 2394.38 +# Mc/sec: 2333.74 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5214,8 +5250,8 @@ 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: 1378.07 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 569.31 // Query: MatE [M=161] Accession: PF01554.17 @@ -5299,8 +5335,8 @@ 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: 683.79 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 887.62 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5337,8 +5373,8 @@ 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: 3657.18 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 4014.57 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5512,8 +5548,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 283.80 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.05 +# Mc/sec: 188.29 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5556,7 +5592,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2426.50 +# Mc/sec: 2871.78 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5612,8 +5648,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 574.55 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1370.42 // Query: MIP [M=227] Accession: PF00230.19 @@ -5664,7 +5700,7 @@ 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: 1836.78 +# Mc/sec: 1015.68 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5717,7 +5753,7 @@ 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: 1160.68 +# Mc/sec: 469.62 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5807,8 +5843,8 @@ 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: 1015.06 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 849.01 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5845,8 +5881,8 @@ 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: 920.82 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 437.81 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5884,7 +5920,7 @@ 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: 1502.08 +# Mc/sec: 1513.12 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5937,7 +5973,7 @@ 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: 1542.08 +# Mc/sec: 986.89 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5974,8 +6010,8 @@ 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: 1976.30 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1901.84 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6096,7 +6132,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 900.98 +# Mc/sec: 589.51 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6147,7 +6183,7 @@ 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: 1514.00 +# Mc/sec: 1319.02 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6217,8 +6253,8 @@ 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: 1049.65 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1792.30 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6270,8 +6306,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 504.00 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 662.96 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6333,8 +6369,8 @@ 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: 1399.11 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 805.24 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6436,8 +6472,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 -# Mc/sec: 139.11 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 183.48 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6484,8 +6520,8 @@ 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: 1129.89 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1684.13 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6536,7 +6572,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 688.74 +# Mc/sec: 169.67 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6587,7 +6623,7 @@ 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: 466.73 +# Mc/sec: 349.24 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6638,7 +6674,7 @@ 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: 1577.00 +# Mc/sec: 1460.80 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6683,7 +6719,7 @@ 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: 1881.34 +# Mc/sec: 1191.01 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6729,8 +6765,8 @@ 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: 686.19 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 154.60 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6795,7 +6831,7 @@ 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: 454.54 +# Mc/sec: 447.08 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6839,8 +6875,8 @@ 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: 1186.05 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 156.02 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6893,7 +6929,7 @@ 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: 468.41 +# Mc/sec: 604.81 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6937,8 +6973,8 @@ 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: 2140.73 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 550.98 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7038,8 +7074,8 @@ 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: 00:00:00.04 -# Mc/sec: 335.08 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.04 +# Mc/sec: 297.74 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7084,7 +7120,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 429.03 +# Mc/sec: 410.73 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7137,7 +7173,7 @@ 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: 1306.89 +# Mc/sec: 2129.40 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7210,8 +7246,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 260.15 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 +# Mc/sec: 258.97 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7272,7 +7308,7 @@ 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: 1094.18 +# Mc/sec: 1519.09 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7316,8 +7352,8 @@ 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: 1552.19 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 406.76 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7369,8 +7405,8 @@ 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: 1151.94 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 677.89 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7408,7 +7444,7 @@ 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: 2847.29 +# Mc/sec: 2782.24 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7451,7 +7487,7 @@ 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: 1463.90 +# Mc/sec: 1194.05 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7513,8 +7549,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 -# Mc/sec: 530.08 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 +# Mc/sec: 469.31 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7552,7 +7588,7 @@ 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: 1976.55 +# Mc/sec: 1571.45 // Query: Usher [M=551] Accession: PF00577.19 @@ -7596,8 +7632,8 @@ 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: 1923.99 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1563.29 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7644,7 +7680,7 @@ 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: 625.95 +# Mc/sec: 173.60 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7688,8 +7724,8 @@ 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: 612.76 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 97.43 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7734,7 +7770,7 @@ 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: 675.63 +# Mc/sec: 197.04 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7789,7 +7825,7 @@ 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: 474.98 +# Mc/sec: 219.39 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7827,8 +7863,8 @@ 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: 308.25 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 319.09 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7880,7 +7916,7 @@ 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: 453.34 +# Mc/sec: 284.41 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7928,7 +7964,7 @@ 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: 699.77 +# Mc/sec: 252.99 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7967,14 +8003,14 @@ 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: 682.94 +# Mc/sec: 290.36 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Mon Aug 18 18:22:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon Aug 18 18:22:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue Sep 22 02:53:31 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 +* [Tue Sep 22 02:53:31 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 @@ -8001,39 +8037,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Mon Aug 18 18:22:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Sep 22 02:53:31 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 -* [Mon Aug 18 18:22:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon Aug 18 18:22:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Aug 18 18:22:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Sep 22 02:53:31 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 +* [Tue Sep 22 02:53:31 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 +* [Tue Sep 22 02:53:32 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... -* [Mon Aug 18 18:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Aug 18 18:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Aug 18 18:22:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Sep 22 02:53:32 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* [Tue Sep 22 02:53:33 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 +* [Tue Sep 22 02:53:33 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/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Mon Aug 18 18:22:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:53:58 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 -* [Mon Aug 18 18:22:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Sep 22 02:54:05 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 -* [Mon Aug 18 18:22:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:54:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Aug 18 18:22:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Sep 22 02:54:09 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon Aug 18 18:22:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Sep 22 02:54:11 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 -* [Mon Aug 18 18:22:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Sep 22 02:54:12 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 @@ -8043,33 +8079,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Mon Aug 18 18:22:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Sep 22 02:54:12 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 -* [Mon Aug 18 18:22:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 02:54:40 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 -* [Mon Aug 18 18:22:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Sep 22 02:54:47 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 -* [Mon Aug 18 18:22:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 02:54:49 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 -* [Mon Aug 18 18:22:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Sep 22 02:54:51 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 -* [Mon Aug 18 18:22:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Sep 22 02:54:52 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 -* [Mon Aug 18 18:22:48 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Mon Aug 18 18:22:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed +* [Tue Sep 22 02:54:53 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* [Tue Sep 22 02:54:53 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 -* [Mon Aug 18 18:22:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep +* [Tue Sep 22 02:54:53 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 -* [Mon Aug 18 18:22:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds +* [Tue Sep 22 02:54:53 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.* @@ -8161,7 +8197,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Mon Aug 18 18:22:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat +* [Tue Sep 22 02:54:54 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. @@ -8185,8 +8221,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Mon Aug 18 18:22:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon Aug 18 18:22:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue Sep 22 02:54:59 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 +* [Tue Sep 22 02:54:59 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 @@ -8861,37 +8897,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Mon Aug 18 18:22:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Sep 22 02:55:00 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 -* [Mon Aug 18 18:22:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores -* [Mon Aug 18 18:22:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Aug 18 18:23:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Sep 22 02:55:00 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 +* [Tue Sep 22 02:55:03 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 +* [Tue Sep 22 02:55:16 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 -* [Mon Aug 18 18:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Aug 18 18:23:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Aug 18 18:23:01 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/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Sep 22 02:55:16 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* [Tue Sep 22 02:55:17 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 +* [Tue Sep 22 02:55:17 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 -* [Mon Aug 18 18:23:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:56:07 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 -* [Mon Aug 18 18:23:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Sep 22 02:56:19 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 -* [Mon Aug 18 18:23:31 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:56:22 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 -* [Mon Aug 18 18:23:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Sep 22 02:56:24 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 -* [Mon Aug 18 18:23:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Sep 22 02:56:26 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 -* [Mon Aug 18 18:23:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Sep 22 02:56:27 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 @@ -8950,33 +8986,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Mon Aug 18 18:23:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Sep 22 02:56:27 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 -* [Mon Aug 18 18:23:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 02:57:13 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/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Mon Aug 18 18:24:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Sep 22 02:57:20 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Mon Aug 18 18:24:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 02:57:22 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 -* [Mon Aug 18 18:24:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Sep 22 02:57:24 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 -* [Mon Aug 18 18:24:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Sep 22 02:57:25 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 -* [Mon Aug 18 18:24:05 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Mon Aug 18 18:24:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed +* [Tue Sep 22 02:57:25 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* [Tue Sep 22 02:57:25 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 -* [Mon Aug 18 18:24:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep +* [Tue Sep 22 02:57:26 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/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Mon Aug 18 18:24:06 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds +* [Tue Sep 22 02:57:26 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/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.* @@ -9069,7 +9105,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Mon Aug 18 18:24:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat +* [Tue Sep 22 02:57:28 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. @@ -9089,8 +9125,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Mon Aug 18 18:24:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon Aug 18 18:24:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue Sep 22 02:57:35 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 +* [Tue Sep 22 02:57:36 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 @@ -9128,37 +9164,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Mon Aug 18 18:24:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Sep 22 02:57:39 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 -* [Mon Aug 18 18:24:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores -* [Mon Aug 18 18:24:13 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/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Aug 18 18:24:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Sep 22 02:57:39 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 +* [Tue Sep 22 02:57:46 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 +* [Tue Sep 22 02:57:59 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 -* [Mon Aug 18 18:24:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Aug 18 18:24:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Aug 18 18:24:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Sep 22 02:57:59 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* [Tue Sep 22 02:57:59 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 +* [Tue Sep 22 02:58:00 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 -* [Mon Aug 18 18:24:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:59:07 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 -* [Mon Aug 18 18:24:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Sep 22 02:59:25 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 -* [Mon Aug 18 18:24:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 02:59:29 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Mon Aug 18 18:24:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Sep 22 02:59:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Mon Aug 18 18:24:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Sep 22 02:59:34 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 -* [Mon Aug 18 18:24:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Sep 22 02:59:36 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 @@ -9264,33 +9300,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Mon Aug 18 18:24:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Sep 22 02:59:37 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 -* [Mon Aug 18 18:25:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:00:43 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 -* [Mon Aug 18 18:25:24 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Sep 22 03:01:00 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 -* [Mon Aug 18 18:25:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:01:03 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 -* [Mon Aug 18 18:25:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Sep 22 03:01:07 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Mon Aug 18 18:25:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Sep 22 03:01:09 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 -* [Mon Aug 18 18:25:27 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Mon Aug 18 18:25:27 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/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed +* [Tue Sep 22 03:01:10 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* [Tue Sep 22 03:01:10 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 -* [Mon Aug 18 18:25:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep +* [Tue Sep 22 03:01:10 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 -* [Mon Aug 18 18:25:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds +* [Tue Sep 22 03:01:11 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.* @@ -9307,9 +9343,8 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp1051_c1_seq1', + 'gene_id' => '', 'trans_id' => '', 'coords' => [ [ @@ -9317,22 +9352,23 @@ '1644586' ] ], + 'asmbl' => 'comp1051_c1_seq1', 'contig' => 'III' }; - num_exons: 1 - source: transdecoder - is_5prime_partial: 0 - TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 - is_3prime_partial: 0 + classification: annotated_genes + gene_length: 1616 is_pseudogene: 0 + is_3prime_partial: 0 + source: transdecoder + gene_type: protein-coding asmbl_id: comp1051_c1_seq1 - mid_pt: 808 - classification: annotated_genes + is_5prime_partial: 0 + num_exons: 1 Model_feat_name: comp1051_c1_seq1.p1 - gene_type: protein-coding - com_name: ORF type:5prime_partial (+),score=83.26 + mid_pt: 808 strand: + - gene_length: 1616 + com_name: ORF type:5prime_partial (+),score=83.26 + TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9349,11 +9385,11 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'orient' => '-', 'gene_id' => '', - 'asmbl' => 'comp1058_c0_seq1', + 'orient' => '-', + 'trans_id' => '', 'contig' => 'I', + 'asmbl' => 'comp1058_c0_seq1', 'coords' => [ [ 5095548, @@ -9365,20 +9401,20 @@ ] ] }; - strand: + - com_name: ORF type:5prime_partial (+),score=32.57 - gene_length: 496 - num_exons: 1 + Model_feat_name: comp1058_c0_seq1.p1 + asmbl_id: comp1058_c0_seq1 + gene_type: protein-coding is_5prime_partial: 0 + num_exons: 1 source: transdecoder - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - is_3prime_partial: 0 is_pseudogene: 0 + is_3prime_partial: 0 classification: annotated_genes - asmbl_id: comp1058_c0_seq1 + gene_length: 496 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + strand: + + com_name: ORF type:5prime_partial (+),score=32.57 mid_pt: 248 - Model_feat_name: comp1058_c0_seq1.p1 - gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9401,6 +9437,9 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', + 'orient' => '-', + 'gene_id' => '', 'coords' => [ [ 2380416, @@ -9412,25 +9451,22 @@ ] ], 'contig' => 'III', - 'trans_id' => '', - 'asmbl' => 'comp1112_c0_seq1', - 'orient' => '-', - 'gene_id' => '' + 'asmbl' => 'comp1112_c0_seq1' }; com_name: ORF type:complete (+),score=155.28 strand: + - gene_length: 2081 - source: transdecoder - is_5prime_partial: 0 - num_exons: 1 + mid_pt: 1041 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 is_3prime_partial: 0 is_pseudogene: 0 - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + gene_length: 2081 + classification: annotated_genes Model_feat_name: comp1112_c0_seq1.p1 + source: transdecoder asmbl_id: comp1112_c0_seq1 - mid_pt: 1041 - classification: annotated_genes gene_type: protein-coding + is_5prime_partial: 0 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -9452,10 +9488,8 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', + 'contig' => 'II', 'asmbl' => 'comp1198_c0_seq1', - 'orient' => '-', - 'gene_id' => '', 'coords' => [ [ 402195, @@ -9474,21 +9508,23 @@ '401683' ] ], - 'contig' => 'II' + 'orient' => '-', + 'gene_id' => '', + 'trans_id' => '' }; - classification: annotated_genes - asmbl_id: comp1198_c0_seq1 + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + strand: + + com_name: ORF type:internal (+),score=37.56 mid_pt: 299 Model_feat_name: comp1198_c0_seq1.p1 + source: transdecoder gene_type: protein-coding - num_exons: 1 + asmbl_id: comp1198_c0_seq1 is_5prime_partial: 0 - source: transdecoder - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - is_3prime_partial: 0 + num_exons: 1 is_pseudogene: 0 - strand: + - com_name: ORF type:internal (+),score=37.56 + is_3prime_partial: 0 + classification: annotated_genes gene_length: 597 gene_synonyms: mRNA_coords @@ -9517,7 +9553,6 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', 'coords' => [ [ 368840, @@ -9528,25 +9563,26 @@ '368790' ] ], - 'orient' => '-', - 'gene_id' => '', 'asmbl' => 'comp1210_c0_seq1', + 'contig' => 'III', + 'gene_id' => '', + 'orient' => '-', 'trans_id' => '' }; + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + mid_pt: 777 com_name: ORF type:5prime_partial (+),score=12.16 strand: + - gene_length: 1554 - Model_feat_name: comp1210_c0_seq1.p1 - asmbl_id: comp1210_c0_seq1 - mid_pt: 777 - classification: annotated_genes - gene_type: protein-coding source: transdecoder + gene_type: protein-coding + asmbl_id: comp1210_c0_seq1 is_5prime_partial: 0 num_exons: 1 + Model_feat_name: comp1210_c0_seq1.p1 + gene_length: 1554 + classification: annotated_genes is_3prime_partial: 0 is_pseudogene: 0 - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9577,26 +9613,26 @@ '3841303' ] ], - 'contig' => 'II', 'asmbl' => 'comp366_c0_seq1', - 'orient' => '-', + 'contig' => 'II', + 'trans_id' => '', 'gene_id' => '', - 'trans_id' => '' + 'orient' => '-' }; - source: transdecoder - is_5prime_partial: 0 - num_exons: 1 - is_pseudogene: 0 - is_3prime_partial: 0 TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - Model_feat_name: comp366_c0_seq1.p1 mid_pt: 170 - asmbl_id: comp366_c0_seq1 - classification: annotated_genes - gene_type: protein-coding com_name: ORF type:internal (-),score=12.83 strand: - + source: transdecoder + num_exons: 1 + is_5prime_partial: 0 + asmbl_id: comp366_c0_seq1 + gene_type: protein-coding + Model_feat_name: comp366_c0_seq1.p1 gene_length: 340 + classification: annotated_genes + is_3prime_partial: 0 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9622,32 +9658,32 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp610_c0_seq1', - 'gene_id' => '', - 'orient' => '-', - 'trans_id' => '', - 'contig' => 'I', 'coords' => [ [ '5471264', '5472770' ] - ] + ], + 'contig' => 'I', + 'asmbl' => 'comp610_c0_seq1', + 'trans_id' => '', + 'gene_id' => '', + 'orient' => '-' }; + source: transdecoder num_exons: 1 is_5prime_partial: 0 - source: transdecoder - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - is_3prime_partial: 0 - is_pseudogene: 0 - classification: annotated_genes asmbl_id: comp610_c0_seq1 - mid_pt: 755 - Model_feat_name: comp610_c0_seq1.p1 gene_type: protein-coding + Model_feat_name: comp610_c0_seq1.p1 + classification: annotated_genes + gene_length: 1509 + is_pseudogene: 0 + is_3prime_partial: 0 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + mid_pt: 755 strand: + com_name: ORF type:5prime_partial (+),score=50.55 - gene_length: 1509 gene_synonyms: mRNA_coords CDS_coords @@ -9672,26 +9708,26 @@ '4336727' ] ], + 'asmbl' => 'comp645_c0_seq1', 'contig' => 'I', 'trans_id' => '', - 'gene_id' => '', 'orient' => '-', - 'asmbl' => 'comp645_c0_seq1' + 'gene_id' => '' }; - is_3prime_partial: 0 - is_pseudogene: 0 - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 - is_5prime_partial: 0 + Model_feat_name: comp645_c0_seq1.p1 source: transdecoder num_exons: 1 + is_5prime_partial: 0 gene_type: protein-coding - Model_feat_name: comp645_c0_seq1.p1 - classification: annotated_genes asmbl_id: comp645_c0_seq1 - mid_pt: 1827 + is_3prime_partial: 0 + is_pseudogene: 0 gene_length: 3653 - strand: + + classification: annotated_genes + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 com_name: ORF type:5prime_partial (+),score=273.35 + strand: + + mid_pt: 1827 gene_synonyms: mRNA_coords CDS_coords @@ -9707,6 +9743,11 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '+', + 'gene_id' => '', + 'trans_id' => '', + 'contig' => 'II', + 'asmbl' => 'comp688_c0_seq1', 'coords' => [ [ 380308, @@ -9716,27 +9757,22 @@ 380624, '381243' ] - ], - 'contig' => 'II', - 'trans_id' => '', - 'asmbl' => 'comp688_c0_seq1', - 'orient' => '+', - 'gene_id' => '' + ] }; - com_name: ORF type:complete (+),score=172.54 - strand: + gene_length: 2784 - asmbl_id: comp688_c0_seq1 - mid_pt: 1392 classification: annotated_genes - Model_feat_name: comp688_c0_seq1.p1 + is_3prime_partial: 0 + is_pseudogene: 0 + asmbl_id: comp688_c0_seq1 gene_type: protein-coding + is_5prime_partial: 0 num_exons: 1 source: transdecoder - is_5prime_partial: 0 + Model_feat_name: comp688_c0_seq1.p1 + mid_pt: 1392 + com_name: ORF type:complete (+),score=172.54 + strand: + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 - is_3prime_partial: 0 - is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9760,11 +9796,11 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', - 'orient' => '+', - 'asmbl' => 'comp856_c0_seq1', 'trans_id' => '', + 'orient' => '+', + 'gene_id' => '', 'contig' => 'II', + 'asmbl' => 'comp856_c0_seq1', 'coords' => [ [ 3753910, @@ -9776,20 +9812,20 @@ ] ] }; - classification: annotated_genes + strand: + + com_name: ORF type:complete (+),score=71.94 mid_pt: 785 - asmbl_id: comp856_c0_seq1 + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + is_pseudogene: 0 + is_3prime_partial: 0 + classification: annotated_genes + gene_length: 1569 Model_feat_name: comp856_c0_seq1.p1 + asmbl_id: comp856_c0_seq1 gene_type: protein-coding num_exons: 1 is_5prime_partial: 0 source: transdecoder - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 - is_pseudogene: 0 - is_3prime_partial: 0 - strand: + - com_name: ORF type:complete (+),score=71.94 - gene_length: 1569 gene_synonyms: mRNA_coords CDS_coords @@ -9809,10 +9845,6 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'gene_id' => '', - 'orient' => '-', - 'asmbl' => 'comp873_c0_seq2', 'coords' => [ [ 3727877, @@ -9827,22 +9859,26 @@ '3727657' ] ], - 'contig' => 'II' + 'contig' => 'II', + 'asmbl' => 'comp873_c0_seq2', + 'orient' => '-', + 'gene_id' => '', + 'trans_id' => '' }; - is_pseudogene: 0 - is_3prime_partial: 0 + mid_pt: 513 + com_name: ORF type:5prime_partial (+),score=8.59 + strand: + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 - source: transdecoder - is_5prime_partial: 0 + gene_length: 1025 + classification: annotated_genes + is_3prime_partial: 0 + is_pseudogene: 0 num_exons: 1 + is_5prime_partial: 0 gene_type: protein-coding - Model_feat_name: comp873_c0_seq2.p1 - mid_pt: 513 asmbl_id: comp873_c0_seq2 - classification: annotated_genes - gene_length: 1025 - com_name: ORF type:5prime_partial (+),score=8.59 - strand: + + source: transdecoder + Model_feat_name: comp873_c0_seq2.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9866,6 +9902,8 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'asmbl' => 'comp888_c0_seq1', + 'contig' => 'III', 'coords' => [ [ 1268244, @@ -9876,26 +9914,24 @@ '1268172' ] ], - 'contig' => 'III', 'trans_id' => '', - 'asmbl' => 'comp888_c0_seq1', 'gene_id' => '', 'orient' => '-' }; - gene_length: 589 - com_name: ORF type:5prime_partial (+),score=23.94 - strand: + - gene_type: protein-coding - Model_feat_name: comp888_c0_seq1.p1 - asmbl_id: comp888_c0_seq1 - mid_pt: 295 classification: annotated_genes - is_3prime_partial: 0 + gene_length: 589 is_pseudogene: 0 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 + is_3prime_partial: 0 source: transdecoder + asmbl_id: comp888_c0_seq1 + gene_type: protein-coding is_5prime_partial: 0 num_exons: 1 + Model_feat_name: comp888_c0_seq1.p1 + mid_pt: 295 + strand: + + com_name: ORF type:5prime_partial (+),score=23.94 + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9917,10 +9953,10 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'trans_id' => '', 'orient' => '+', + 'gene_id' => '', 'asmbl' => 'comp940_c0_seq1', - 'trans_id' => '', 'contig' => 'III', 'coords' => [ [ @@ -9933,20 +9969,20 @@ ] ] }; - num_exons: 1 - is_5prime_partial: 0 - source: transdecoder - TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 is_3prime_partial: 0 is_pseudogene: 0 + gene_length: 2129 classification: annotated_genes - asmbl_id: comp940_c0_seq1 - mid_pt: 1065 Model_feat_name: comp940_c0_seq1.p1 + source: transdecoder gene_type: protein-coding - strand: + + asmbl_id: comp940_c0_seq1 + num_exons: 1 + is_5prime_partial: 0 com_name: ORF type:complete (+),score=94.37 - gene_length: 2129 + strand: + + mid_pt: 1065 + TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9966,6 +10002,11 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', + 'gene_id' => '', + 'orient' => '-', + 'contig' => 'I', + 'asmbl' => 'comp983_c0_seq1', 'coords' => [ [ 4100066, @@ -9975,27 +10016,22 @@ 4098246, '4100014' ] - ], - 'contig' => 'I', - 'asmbl' => 'comp983_c0_seq1', - 'orient' => '-', - 'gene_id' => '', - 'trans_id' => '' + ] }; - gene_length: 1870 - strand: + + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + mid_pt: 935 com_name: ORF type:5prime_partial (+),score=143.65 + strand: + gene_type: protein-coding - Model_feat_name: comp983_c0_seq1.p1 - classification: annotated_genes - mid_pt: 935 asmbl_id: comp983_c0_seq1 - is_pseudogene: 0 - is_3prime_partial: 0 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 is_5prime_partial: 0 - source: transdecoder num_exons: 1 + source: transdecoder + Model_feat_name: comp983_c0_seq1.p1 + gene_length: 1870 + classification: annotated_genes + is_3prime_partial: 0 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -10039,7 +10075,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Mon Aug 18 18:25:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue Sep 22 03:01:15 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. @@ -10064,8 +10100,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Mon Aug 18 18:25:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon Aug 18 18:25:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +* [Tue Sep 22 03:01:48 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 +* [Tue Sep 22 03:01:49 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 @@ -12683,37 +12719,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Mon Aug 18 18:25:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Sep 22 03:01:53 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Mon Aug 18 18:25:46 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon Aug 18 18:25:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Aug 18 18:26:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Sep 22 03:01:53 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores +* [Tue Sep 22 03:02:00 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 +* [Tue Sep 22 03:03:26 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 -* [Mon Aug 18 18:26:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Aug 18 18:26:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Aug 18 18:26:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Sep 22 03:03:27 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* [Tue Sep 22 03:03:27 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 +* [Tue Sep 22 03:03:30 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 -* [Mon Aug 18 18:26:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 03:04:22 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 -* [Mon Aug 18 18:27:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Sep 22 03:04:33 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 -* [Mon Aug 18 18:27:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 03:04:35 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 -* [Mon Aug 18 18:27:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Sep 22 03:04:37 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 -* [Mon Aug 18 18:27:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Sep 22 03:04:38 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 -* [Mon Aug 18 18:27:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Sep 22 03:04:40 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 @@ -12816,33 +12852,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Mon Aug 18 18:27:05 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Sep 22 03:04:41 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 -* [Mon Aug 18 18:27:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:05:31 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 -* [Mon Aug 18 18:27:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Sep 22 03:05:39 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 -* [Mon Aug 18 18:27:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:05:42 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 -* [Mon Aug 18 18:27:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Sep 22 03:05:44 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 -* [Mon Aug 18 18:27:37 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Sep 22 03:05:46 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 -* [Mon Aug 18 18:27:38 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Mon Aug 18 18:27:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed +* [Tue Sep 22 03:05:47 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* [Tue Sep 22 03:05:47 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 -* [Mon Aug 18 18:27:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep +* [Tue Sep 22 03:05:48 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Mon Aug 18 18:27:40 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds +* [Tue Sep 22 03:05:51 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.* @@ -12954,7 +12990,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Mon Aug 18 18:27:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat +* [Tue Sep 22 03:06:05 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. @@ -12978,19 +13014,19 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Mon Aug 18 18:27:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Mon Aug 18 18:27:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr --skipping training candidate: bdg_i2.p1, not unique enough +* [Tue Sep 22 03:06:08 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 +* [Tue Sep 22 03:06:08 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_i3.p1, not unique enough -skipping training candidate: bdg_i4.p1, not unique enough -skipping training candidate: bdg_i1.p1, not unique enough -skipping training candidate: Dgk_i7.p1, not unique enough -skipping training candidate: Cdep_i1.p1, not unique enough --skipping training candidate: eIF5B_i4.p1, not unique enough -skipping training candidate: eIF5B_i2.p1, not unique enough +-skipping training candidate: eIF5B_i3.p1, not unique enough -skipping training candidate: 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 @@ -13000,36 +13036,36 @@ -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough --skipping training candidate: Calx_i5.p1, not unique enough --skipping training candidate: Calx_i4.p1, not unique enough -skipping training candidate: Calx_i2.p1, not unique enough +-skipping training candidate: Calx_i5.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: cdi_i1.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough --skipping training candidate: Klp10A_i5.p1, not unique enough +-skipping training candidate: Klp10A_i4.p1, not unique enough +-skipping training candidate: Klp10A_i2.p1, not unique enough -skipping training candidate: Klp10A_i6.p1, not unique enough -skipping training candidate: Klp10A_i3.p1, not unique enough --skipping training candidate: Klp10A_i2.p1, not unique enough --skipping training candidate: Klp10A_i1.p1, not unique enough --skipping training candidate: CG6424_i3.p1, not unique enough +-skipping training candidate: Klp10A_i5.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough +-skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough -skipping training candidate: CG33970_i2.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough --skipping training candidate: CG12581_i2.p1, not unique enough --skipping training candidate: CG6091_i1.p1, not unique enough +-skipping training candidate: CG12581_i1.p1, not unique enough +-skipping training candidate: CG6091_i3.p1, not unique enough -skipping training candidate: hrg_i2.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_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough --skipping training candidate: Npl4_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 @@ -13044,159 +13080,159 @@ -skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough --skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough +-skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Est-6_i2.p1, not unique enough --skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: S-Lap3_i3.p1, not unique enough +-skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough --skipping training candidate: CG30438_i5.p1, not unique enough --skipping training candidate: CG30438_i1.p1, not unique enough +-skipping training candidate: CG30438_i3.p1, not unique enough -skipping training candidate: CG30438_i2.p1, not unique enough +-skipping training candidate: CG30438_i1.p1, not unique enough -skipping training candidate: CG6145_i4.p1, not unique enough -skipping training candidate: CG33970_i3.p1, not unique enough -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough --skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i5.p1, not unique enough +-skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i3.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough --skipping training candidate: Aldh-III_i3.p1, not unique enough +-skipping training candidate: Aldh-III_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_i6.p1, not unique enough --skipping training candidate: Aldh-III_i10.p1, not unique enough +-skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Aldh-III_i10.p1, not unique enough +-skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough --skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: 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_i4.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_i3.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: CG6424_i2.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_i4.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: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough --skipping training candidate: AdipoR_i2.p1, not unique enough --skipping training candidate: AdipoR_i5.p1, not unique enough -skipping training candidate: AdipoR_i4.p1, not unique enough --skipping training candidate: Tm1_i5.p1, not unique enough +-skipping training candidate: AdipoR_i5.p1, not unique enough +-skipping training candidate: AdipoR_i3.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough +-skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough --skipping training candidate: kto_i1.p2, not unique enough +-skipping training candidate: kto_i2.p3, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough --skipping training candidate: nmo_i1.p1, not unique enough +-skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough --skipping training candidate: CG7564_i3.p1, not unique enough --skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG7564_i4.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: CG14995_i7.p1, not unique enough --skipping training candidate: nmo_i2.p1, not unique enough -skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i5.p1, not unique enough +-skipping training candidate: nmo_i2.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough --skipping training candidate: CG6024_i2.p1, not unique enough +-skipping training candidate: CG6024_i1.p1, not unique enough -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough --skipping training candidate: ogre_i2.p1, not unique enough --skipping training candidate: ogre_i6.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_i6.p1, not unique enough +-skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: ogre_i4.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough --skipping training candidate: Gale_i1.p1, not unique enough +-skipping training candidate: Gale_i2.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough --skipping training candidate: CG13284_i3.p1, not unique enough +-skipping training candidate: CG13284_i5.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_i4.p2, not unique enough +-skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Klp10A_i6.p2, not unique enough -skipping training candidate: Klp10A_i3.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: Calx_i7.p2, not unique enough --skipping training candidate: sqd_i2.p1, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough --skipping training candidate: CG10237_i5.p1, not unique enough +-skipping training candidate: sqd_i2.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_i4.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough -skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough +-skipping training candidate: l(3)05822_i1.p2, not unique enough -skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: l(3)05822_i3.p2, not unique enough --skipping training candidate: l(3)05822_i2.p2, not unique enough --skipping training candidate: Tm1_i11.p1, not unique enough --skipping training candidate: Tm1_i9.p1, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough --skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Tm1_i3.p1, not unique enough +-skipping training candidate: Tm1_i9.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough --skipping training candidate: Npl4_i1.p2, not unique enough +-skipping training candidate: Tm1_i4.p1, not unique enough +-skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Npl4_i3.p2, not unique enough --skipping training candidate: Sec16_i1.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_i5.p2, not unique enough +-skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: eIF5B_i4.p2, not unique enough --skipping training candidate: eIF5B_i1.p2, not unique enough -skipping training candidate: eIF5B_i2.p2, not unique enough +-skipping training candidate: eIF5B_i3.p2, not unique enough +-skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: Dgk_i6.p2, not unique enough -skipping training candidate: Dgk_i3.p2, not unique enough --skipping training candidate: l(1)G0193_i2.p2, not unique enough +-skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: l(1)G0193_i1.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough --skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i4.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_i3.p3, not unique enough --skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough --skipping training candidate: CG6024_i2.p2, not unique enough +-skipping training candidate: CG6024_i1.p2, not unique enough -skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: Sec16_i5.p3, not unique enough --skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG13887_i4.p1, not unique enough +-skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough --skipping training candidate: nmo_i7.p2, not unique enough --skipping training candidate: nmo_i6.p2, not unique enough --skipping training candidate: nmo_i3.p2, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough +-skipping training candidate: nmo_i6.p2, not unique enough -skipping training candidate: nmo_i5.p2, not unique enough +-skipping training candidate: nmo_i3.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough +-skipping training candidate: nmo_i2.p2, not unique enough -skipping training candidate: 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 @@ -13204,205 +13240,205 @@ -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_i3.p1, not unique enough --skipping training candidate: RpL15_i4.p1, not unique enough -skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough --skipping training candidate: Npl4_i1.p3, not unique enough +-skipping training candidate: RpL15_i4.p1, not unique enough +-skipping training candidate: RpL15_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p3, not unique enough +-skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: trc_i2.p2, not unique enough --skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough +-skipping training candidate: Hsc70-1_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough +-skipping training candidate: CG10237_i3.p2, not unique enough -skipping training candidate: CG10237_i5.p2, not unique enough --skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: CG10237_i1.p2, not unique enough --skipping training candidate: CG10237_i4.p2, not unique enough --skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i4.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_i3.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Eno_i6.p3, not unique enough --skipping training candidate: Sec16_i3.p2, not unique enough +-skipping training candidate: Sec16_i1.p3, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough --skipping training candidate: gukh_i1.p3, not unique enough --skipping training candidate: ATPsyn-d_i3.p1, not unique enough +-skipping training candidate: gukh_i2.p2, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough +-skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough --skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG30438_i5.p2, not unique enough --skipping training candidate: CG30438_i1.p2, not unique enough +-skipping training candidate: CG30438_i3.p2, not unique enough -skipping training candidate: CG30438_i2.p2, not unique enough +-skipping training candidate: CG30438_i1.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough --skipping training candidate: cdi_i2.p2, not unique enough +-skipping training candidate: cdi_i1.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough --skipping training candidate: CanB2_i1.p1, 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_i1.p4, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: bic_i2.p1, not unique enough --skipping training candidate: CG12581_i2.p2, not unique enough +-skipping training candidate: bic_i1.p1, not unique enough +-skipping training candidate: CG12581_i1.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i2.p1, not unique enough -skipping training candidate: ctp_i1.p1, not unique enough +-skipping training candidate: ctp_i2.p1, not unique enough -skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough --skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i4.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_i3.p4, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough --skipping training candidate: Klp10A_i5.p3, not unique enough +-skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Klp10A_i2.p4, not unique enough -skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i3.p3, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough --skipping training candidate: Klp10A_i1.p3, not unique enough +-skipping training candidate: Klp10A_i5.p3, not unique enough +-skipping training candidate: Calx_i6.p2, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i4.p2, not unique enough --skipping training candidate: Calx_i9.p2, not unique enough --skipping training candidate: Calx_i2.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_i3.p2, not unique enough --skipping training candidate: Calx_i6.p2, not unique enough --skipping training candidate: CG7564_i1.p2, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough --skipping training candidate: CG7564_i2.p4, not unique enough --skipping training candidate: CG7564_i2.p5, not unique enough +-skipping training candidate: Calx_i8.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough +-skipping training candidate: Calx_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough --skipping training candidate: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i5.p3, not unique enough +-skipping training candidate: CG7564_i2.p4, not unique enough +-skipping training candidate: CG7564_i2.p5, not unique enough +-skipping training candidate: CG7564_i1.p2, not unique enough +-skipping training candidate: CG7564_i1.p3, not unique enough +-skipping training candidate: Gale_i2.p2, not unique enough -skipping training candidate: eIF5B_i4.p3, not unique enough --skipping training candidate: eIF5B_i1.p3, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough +-skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough --skipping training candidate: AdipoR_i4.p2, not unique enough +-skipping training candidate: AdipoR_i3.p2, not unique enough -skipping training candidate: CG6424_i2.p3, not unique enough --skipping training candidate: CG6424_i1.p3, not unique enough --skipping training candidate: CG6424_i1.p4, not unique enough -skipping training candidate: CG6424_i4.p3, not unique enough --skipping training candidate: Tm1_i13.p2, 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_i5.p2, not unique enough -skipping training candidate: Tm1_i16.p2, not unique enough --skipping training candidate: Tm1_i14.p2, not unique enough +-skipping training candidate: Tm1_i13.p2, not unique enough -skipping training candidate: Dgk_i7.p5, not unique enough --skipping training candidate: Dgk_i6.p4, not unique enough -skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i6.p4, not unique enough -skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: cdi_i2.p3, not unique enough +-skipping training candidate: cdi_i1.p4, not unique enough -skipping training candidate: eff_i2.p1, not unique enough -skipping training candidate: eff_i1.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i5.p4, not unique enough -skipping training candidate: eIF5B_i4.p5, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough +-skipping training candidate: eIF5B_i3.p4, not unique enough +-skipping training candidate: eIF5B_i5.p4, not unique enough -skipping training candidate: Sec16_i3.p4, not unique enough --skipping training candidate: Sec16_i6.p3, not unique enough --skipping training candidate: Sec16_i4.p5, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough -skipping training candidate: Sec16_i5.p4, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: Sec16_i4.p5, not unique enough +-skipping training candidate: CG32082_i3.p2, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough -skipping training candidate: CG32082_i1.p2, not unique enough --skipping training candidate: CG32082_i2.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough --skipping training candidate: CG3530_i1.p2, not unique enough +-skipping training candidate: CG3530_i2.p2, not unique enough -skipping training candidate: Dgk_i7.p6, not unique enough +-skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough --skipping training candidate: l(3)05822_i2.p4, not unique enough --skipping training candidate: sqd_i1.p2, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough --skipping training candidate: CG7564_i2.p6, not unique enough +-skipping training candidate: sqd_i2.p2, not unique enough -skipping training candidate: CG7564_i4.p4, not unique enough --skipping training candidate: S-Lap3_i2.p2, not unique enough +-skipping training candidate: CG7564_i2.p6, not unique enough +-skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough --skipping training candidate: cdi_i2.p4, not unique enough +-skipping training candidate: S-Lap3_i2.p2, not unique enough +-skipping training candidate: cdi_i1.p5, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough --skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: CG6091_i4.p2, not unique enough +-skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough --skipping training candidate: Cnx99A_i3.p2, not unique enough --skipping training candidate: Cnx99A_i1.p2, not unique enough -skipping training candidate: Cnx99A_i4.p2, not unique enough +-skipping training candidate: Cnx99A_i2.p2, not unique enough +-skipping training candidate: Cnx99A_i1.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_i5.p5, not unique enough --skipping training candidate: ogre_i3.p2, not unique enough --skipping training candidate: CG6024_i2.p3, not unique enough --skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: ogre_i6.p2, not unique enough +-skipping training candidate: CG6024_i1.p3, not unique enough -skipping training candidate: hrg_i1.p3, not unique enough --skipping training candidate: ATPsyn-d_i1.p2, not unique enough --skipping training candidate: CG6091_i1.p3, not unique enough +-skipping training candidate: hrg_i4.p3, not unique enough +-skipping training candidate: ATPsyn-d_i3.p2, not unique enough -skipping training candidate: CG6091_i4.p3, not unique enough +-skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough -skipping training candidate: CG33970_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_i3.p5, not unique enough -skipping training candidate: eIF5B_i5.p5, not unique enough --skipping training candidate: eIF5B_i1.p5, not unique enough --skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: Aldh-III_i8.p2, not unique enough --skipping training candidate: CG13284_i2.p2, not unique enough --skipping training candidate: CG13284_i1.p2, not unique enough --skipping training candidate: CG13284_i5.p2, not unique enough +-skipping training candidate: Aldh-III_i10.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough --skipping training candidate: Lip4_i1.p2, not unique enough +-skipping training candidate: CG13284_i4.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: Lip4_i3.p2, not unique enough -skipping training candidate: Lip4_i2.p2, not unique enough -skipping training candidate: Dgk_i7.p7, not unique enough --skipping training candidate: Dgk_i6.p5, not unique enough -skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Dgk_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_i1.p5, not unique enough --skipping training candidate: Dgk_i5.p4, not unique enough --skipping training candidate: Tm1_i13.p3, not unique enough +-skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: Tm1_i16.p3, not unique enough --skipping training candidate: Tm1_i14.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: Tm1_i13.p3, not unique enough -skipping training candidate: CG8312_i2.p3, not unique enough -skipping training candidate: CG8312_i2.p4, not unique enough -skipping training candidate: CG8312_i4.p3, not unique enough -skipping training candidate: CG8312_i4.p4, not unique enough --skipping training candidate: Klp10A_i5.p4, not unique enough +-skipping training candidate: CG8312_i3.p3, not unique enough +-skipping training candidate: CG8312_i3.p4, not unique enough +-skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: Klp10A_i2.p6, not unique enough -skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i3.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough --skipping training candidate: Klp10A_i1.p4, not unique enough +-skipping training candidate: Klp10A_i5.p4, not unique enough -skipping training candidate: eff_i2.p2, not unique enough -skipping training candidate: eff_i1.p2, not unique enough -skipping training candidate: CG14995_i5.p5, not unique enough +-skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG14995_i7.p4, not unique enough --skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG14995_i3.p4, not unique enough +-skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG6424_i2.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: CG12581_i2.p3, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough +-skipping training candidate: CG12581_i1.p3, not unique enough +-skipping training candidate: CG32082_i3.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: CG32082_i1.p3, not unique enough --skipping training candidate: CG32082_i2.p3, not unique enough --skipping training candidate: Cnx99A_i3.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p3, not unique enough -skipping training candidate: Cnx99A_i1.p3, not unique enough -skipping training candidate: Cdep_i2.p6, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough @@ -13410,265 +13446,266 @@ -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_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_i5.p6, not unique enough +-skipping training candidate: Sec16_i1.p7, not unique enough +-skipping training candidate: Sec16_i4.p6, not unique enough +-skipping training candidate: Sec16_i4.p7, not unique enough -skipping training candidate: mge_i3.p1, not unique enough --skipping training candidate: CG6024_i2.p4, not unique enough --skipping training candidate: Myo61F_i2.p2, not unique enough --skipping training candidate: Myo61F_i1.p2, not unique enough +-skipping training candidate: CG6024_i1.p4, not unique enough -skipping training candidate: Myo61F_i4.p2, not unique enough +-skipping training candidate: Myo61F_i2.p2, not unique enough +-skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i3.p4, not unique enough +-skipping training candidate: Cnx99A_i2.p4, not unique enough -skipping training candidate: Cnx99A_i1.p4, not unique enough --skipping training candidate: CG13887_i1.p2, not unique enough -skipping training candidate: CG13887_i4.p2, not unique enough --skipping training candidate: CG6145_i2.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough +-skipping training candidate: CG13887_i1.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG6145_i2.p2, not unique enough -skipping training candidate: CG6145_i4.p2, not unique enough +-skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i4.p3, not unique enough --skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i2.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_i3.p3, not unique enough --skipping training candidate: Calx_i6.p3, not unique enough --skipping training candidate: mge_i2.p2, not unique enough --skipping training candidate: AdipoR_i3.p3, not unique enough +-skipping training candidate: Calx_i8.p3, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough +-skipping training candidate: Calx_i4.p3, not unique enough +-skipping training candidate: mge_i1.p2, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i4.p3, not unique enough --skipping training candidate: Aldh-III_i2.p2, not unique enough +-skipping training candidate: AdipoR_i5.p2, not unique enough +-skipping training candidate: AdipoR_i3.p3, not unique enough -skipping training candidate: Aldh-III_i1.p2, not unique enough -skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough +-skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i9.p2, not unique enough +-skipping training candidate: Aldh-III_i2.p2, not unique enough -skipping training candidate: Cdep_i2.p9, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough --skipping training candidate: CG33125_i1.p3, not unique enough +-skipping training candidate: hrg_i4.p4, not unique enough +-skipping training candidate: CG33125_i2.p2, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough --skipping training candidate: CG12581_i2.p4, not unique enough +-skipping training candidate: CG12581_i1.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_i6.p6, not unique enough --skipping training candidate: Sec16_i6.p7, 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: Sec16_i5.p7, not unique enough -skipping training candidate: Sec16_i5.p8, not unique enough +-skipping training candidate: Sec16_i1.p8, not unique enough +-skipping training candidate: Sec16_i1.p9, not unique enough +-skipping training candidate: Sec16_i4.p8, not unique enough +-skipping training candidate: Sec16_i4.p9, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough --skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i4.p4, not unique enough --skipping training candidate: CanB2_i1.p2, not unique enough +-skipping training candidate: CG6091_i3.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_i4.p5, not unique enough +-skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i3.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: AdipoR_i2.p3, not unique enough -skipping training candidate: Cdep_i2.p10, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough -skipping training candidate: Est-6_i2.p2, not unique enough --skipping training candidate: Klp10A_i5.p6, not unique enough +-skipping training candidate: Klp10A_i4.p6, not unique enough +-skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: Klp10A_i6.p6, not unique enough -skipping training candidate: Klp10A_i3.p6, not unique enough --skipping training candidate: Klp10A_i2.p9, not unique enough --skipping training candidate: Klp10A_i1.p7, not unique enough +-skipping training candidate: Klp10A_i5.p6, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i3.p5, not unique enough --skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Cnx99A_i4.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: Cnx99A_i2.p5, not unique enough +-skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Myo61F_i4.p3, 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_i2.p3, not unique enough +-skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i4.p4, not unique enough --skipping training candidate: bic_i2.p2, not unique enough +-skipping training candidate: Myo61F_i2.p4, not unique enough +-skipping training candidate: Myo61F_i3.p4, not unique enough +-skipping training candidate: bic_i1.p3, not unique enough -skipping training candidate: CG10082_i2.p3, not unique enough +-skipping training candidate: CG32082_i3.p4, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough -skipping training candidate: CG32082_i1.p4, not unique enough --skipping training candidate: CG32082_i2.p4, not unique enough --skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i4.p6, 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_i3.p5, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough --skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough +-skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Dgk_i7.p8, not unique enough --skipping training candidate: Dgk_i6.p6, not unique enough -skipping training candidate: Dgk_i3.p6, not unique enough +-skipping training candidate: Dgk_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_i1.p6, not unique enough --skipping training candidate: Dgk_i5.p5, not unique enough --skipping training candidate: nmo_i4.p3, not unique enough +-skipping training candidate: nmo_i6.p3, not unique enough -skipping training candidate: CG33970_i2.p5, not unique enough --skipping training candidate: sqd_i5.p3, not unique enough --skipping training candidate: Dgk_i3.p7, not unique enough +-skipping training candidate: sqd_i3.p2, not unique enough +-skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: Dgk_i1.p7, not unique enough --skipping training candidate: His4r_i2.p1, not unique enough --skipping training candidate: His4r_i4.p1, not unique enough +-skipping training candidate: His4r_i3.p1, not unique enough -skipping training candidate: His4r_i1.p1, not unique enough --skipping training candidate: Hsc70-1_i1.p4, not unique enough +-skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough --skipping training candidate: hrg_i4.p6, not unique enough +-skipping training candidate: Hsc70-1_i3.p4, not unique enough -skipping training candidate: hrg_i1.p5, not unique enough +-skipping training candidate: hrg_i4.p6, not unique enough -skipping training candidate: CG8136_i3.p2, not unique enough -skipping training candidate: CG8136_i2.p2, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough --skipping training candidate: Myo61F_i2.p5, not unique enough --skipping training candidate: Myo61F_i1.p5, not unique enough -skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: Myo61F_i2.p5, not unique enough +-skipping training candidate: Myo61F_i3.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_i4.p5, not unique enough --skipping training candidate: CG6145_i2.p3, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: CG6091_i3.p5, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i4.p3, not unique enough --skipping training candidate: gukh_i1.p4, not unique enough --skipping training candidate: sqd_i5.p4, not unique enough --skipping training candidate: CG33125_i1.p4, not unique enough --skipping training candidate: gukh_i1.p5, not unique enough +-skipping training candidate: CG6145_i1.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: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Mon Aug 18 18:27:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest +* [Tue Sep 22 03:06:09 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 -* [Mon Aug 18 18:27:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores -* [Mon Aug 18 18:27:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores -* [Mon Aug 18 18:27:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Sep 22 03:06:09 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 +* [Tue Sep 22 03:06:11 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 +* [Tue Sep 22 03:06:19 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 -* [Mon Aug 18 18:27:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Mon Aug 18 18:27:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Mon Aug 18 18:27:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Sep 22 03:06:20 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* [Tue Sep 22 03:06:20 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 +* [Tue Sep 22 03:06:20 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 -* [Mon Aug 18 18:28:21 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/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 03:07:03 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 -* [Mon Aug 18 18:28:27 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Sep 22 03:07:10 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 -* [Mon Aug 18 18:28:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Sep 22 03:07:11 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 -* [Mon Aug 18 18:28:29 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Sep 22 03:07:13 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 -* [Mon Aug 18 18:28:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Sep 22 03:07:14 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 -* [Mon Aug 18 18:28:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced +* [Tue Sep 22 03:07:14 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: -1.46720733237519 instead of -3.57097560839711 --feature swap of score: -1.47904833582865 instead of -3.30198186892269 --feature swap of score: -1.89368395647714 instead of -2.94611306928203 --feature swap of score: -1.38001307560883 instead of -1.60038048816474 --feature swap of score: -0.81738947106451 instead of -1.29792189304816 --feature swap of score: -0.442441838711206 instead of -1.0802627920382 --feature swap of score: 1.96510181685696 instead of -1.0361919192427 --feature swap of score: -0.593298345611315 instead of -1.20723035644037 --feature swap of score: 2.82037688527289 instead of -1.01330968825716 --feature swap of score: -0.955067397147497 instead of -2.47186066088463 --feature swap of score: 2.12939585012796 instead of -1.26018862457858 --feature swap of score: -0.623148708413847 instead of -1.17140652014558 --feature swap of score: 0.39154341107981 instead of -1.49083383596816 --feature swap of score: 1.10672212330994 instead of -0.879807889143032 --feature swap of score: 1.99744259548033 instead of -1.17605701833117 --feature swap of score: -0.868737192891573 instead of -1.05483227508497 --feature swap of score: 0.0420694110765515 instead of -1.35142468302219 --feature swap of score: -0.563887936602345 instead of -1.14472425532965 --feature swap of score: -0.190636528475061 instead of -1.22475520331621 --feature swap of score: 0.34357051983745 instead of -0.626958938780869 --feature swap of score: 0.647207156164645 instead of -0.528543309219941 --feature swap of score: 3.35092419708115 instead of -0.480501302497246 --feature swap of score: 1.77913401286257 instead of -0.195838649685368 --feature swap of score: -0.0701823989781382 instead of -0.571675731956758 --feature swap of score: 2.79569737840889 instead of -1.03929923155324 --feature swap of score: -0.527384195827072 instead of -0.706396185552927 --feature swap of score: 1.49261152969141 instead of -0.0874122000552275 --feature swap of score: 1.30410960729325 instead of 0.00562081917298873 --feature swap of score: 0.891338058874364 instead of -0.00209893407155659 --feature swap of score: 2.01575304924767 instead of -0.221626656577502 --feature swap of score: 0.21669173602913 instead of 0.0863915536370607 --feature swap of score: 0.41206335042563 instead of -0.107935170598443 --feature swap of score: 0.753213701229941 instead of -0.125795186861498 --feature swap of score: 0.0853243571898894 instead of -0.473951822186296 --feature swap of score: 0.949267347765409 instead of -0.663841065159027 --feature swap of score: -0.245752259654993 instead of -0.579638569428033 --feature swap of score: 0.262064861954058 instead of -0.735136965628896 --feature swap of score: 1.52499444338816 instead of -0.449592258039778 --feature swap of score: 0.0559638202501467 instead of -0.338075184743988 --feature swap of score: 1.64037481500493 instead of -0.152089270215074 --feature swap of score: 0.696786468064694 instead of -0.156494142879963 --feature swap of score: 0.387976953611751 instead of -0.194081330910774 --feature swap of score: 1.43335684797173 instead of -0.141426784888927 --feature swap of score: 1.34335320690329 instead of 0.236214304170289 --feature swap of score: 1.38787037194283 instead of -0.0104922119521395 --feature swap of score: 0.689824525257401 instead of 0.0320529551657628 --feature swap of score: 0.905996654790921 instead of 0.0177980961499384 --feature swap of score: 3.39555867723059 instead of -0.0365788253013512 --feature swap of score: 2.20931841697902 instead of 0.502017646526833 --feature swap of score: 3.06230553017875 instead of -0.765163477660566 --feature swap of score: 1.03443632933731 instead of -0.0581789543940497 --feature swap of score: 2.42586397741008 instead of -0.108554729122308 --feature swap of score: 4.68120564415537 instead of 0.294451668869494 --feature swap of score: 1.13061602171559 instead of 0.0623143829193307 --feature swap of score: 5.97731209628149 instead of 0.451216884737171 --feature swap of score: 3.27693803916342 instead of 0.369852684869464 --num feature swaps: 56 -* [Mon Aug 18 18:28:30 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: -1.40912367928079 instead of -3.43465830145101 +-feature swap of score: -1.30964663606972 instead of -3.46640715643693 +-feature swap of score: -1.95938219527711 instead of -3.08618101630309 +-feature swap of score: -1.50393312640155 instead of -1.64693822502656 +-feature swap of score: -0.97892749019659 instead of -1.4065791388601 +-feature swap of score: -0.617416958075086 instead of -1.43816577691354 +-feature swap of score: 2.00765156451152 instead of -1.09994916201273 +-feature swap of score: -0.511957862169612 instead of -1.03993420056077 +-feature swap of score: 2.76329806318566 instead of -1.06602634446385 +-feature swap of score: -0.927858743695941 instead of -2.51975289664972 +-feature swap of score: 2.08661060677722 instead of -1.1285386854515 +-feature swap of score: -0.771232464999037 instead of -1.13724794659245 +-feature swap of score: 0.206795964253161 instead of -1.27047111201955 +-feature swap of score: 1.03560367489271 instead of -0.871807290304847 +-feature swap of score: 1.87459173502072 instead of -1.1057268049678 +-feature swap of score: -1.14006154527001 instead of -1.16699851929169 +-feature swap of score: 0.217836327577935 instead of -1.32414164293861 +-feature swap of score: -0.30968051091675 instead of -1.31166806649052 +-feature swap of score: -0.00234735877963377 instead of -1.00045717676477 +-feature swap of score: 0.19967202247783 instead of -0.571134455550273 +-feature swap of score: 0.298801229096646 instead of -0.667663750527128 +-feature swap of score: 3.3699649512286 instead of -0.622599063416611 +-feature swap of score: 2.27610570257077 instead of -0.431398362492735 +-feature swap of score: 0.429166423265592 instead of -0.524986215498902 +-feature swap of score: 2.23055171034107 instead of -0.487986771480392 +-feature swap of score: -0.530115703219542 instead of -0.579168295233343 +-feature swap of score: 0.00174582118010802 instead of -0.258058893645557 +-feature swap of score: 1.34117860740184 instead of -0.140323715592359 +-feature swap of score: 1.02027824705328 instead of -0.251525376296023 +-feature swap of score: 0.418887875102581 instead of -0.29338898497678 +-feature swap of score: 2.56885558127253 instead of -0.189650507550847 +-feature swap of score: 0.569572600776081 instead of -0.374630304517412 +-feature swap of score: 0.323481135132386 instead of -0.428712590241275 +-feature swap of score: -0.248002390207638 instead of -0.537564584361658 +-feature swap of score: -0.70544448479953 instead of -0.713629284455502 +-feature swap of score: -0.0964814787417578 instead of -0.423622956542431 +-feature swap of score: 0.492289166184967 instead of -0.556190546113813 +-feature swap of score: -0.283637105584353 instead of -0.378262799210195 +-feature swap of score: 2.77386211434538 instead of -0.412366451909516 +-feature swap of score: 1.37047322855369 instead of -0.218705684888523 +-feature swap of score: 1.7881323858018 instead of -0.289165824439231 +-feature swap of score: 0.341000162205124 instead of -0.402820111832599 +-feature swap of score: 1.39999843929822 instead of -0.355614008833046 +-feature swap of score: 0.879529098443085 instead of -0.389021912493896 +-feature swap of score: 1.07235839364306 instead of 0.394904617333149 +-feature swap of score: 1.36169472822072 instead of -0.681408463738615 +-feature swap of score: 1.03197046579623 instead of 0.13027933214558 +-feature swap of score: 0.296071877250246 instead of 0.14870129629813 +-feature swap of score: 3.29243671361231 instead of 0.425181380019697 +-feature swap of score: 2.07847678142773 instead of 0.581320320675866 +-feature swap of score: 2.89065896027029 instead of 0.317476343265326 +-feature swap of score: 1.12727987187791 instead of 0.29362393006066 +-feature swap of score: 2.36396077241654 instead of 0.326108600847481 +-feature swap of score: 4.93154575241936 instead of 0.537422974005974 +-feature swap of score: 1.70020013918292 instead of 0.451823241876155 +-feature swap of score: 5.69013192510464 instead of 0.894735602697453 +-feature swap of score: 3.10891621576248 instead of 0.494977190189838 +-num feature swaps: 57 +* [Tue Sep 22 03:07:15 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 -* [Mon Aug 18 18:28:54 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:07:44 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 -* [Mon Aug 18 18:28:59 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.enhanced.feature.scores.roc || : +* [Tue Sep 22 03:07:56 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 -* [Mon Aug 18 18:29:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Sep 22 03:07:59 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 -* [Mon Aug 18 18:29:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Sep 22 03:08:01 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 -* [Mon Aug 18 18:29:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 +* [Tue Sep 22 03:08:02 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: 13 -* [Mon Aug 18 18:29:02 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 -copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Mon Aug 18 18:29:02 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 +* [Tue Sep 22 03:08:03 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* [Tue Sep 22 03:08:03 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 -* [Mon Aug 18 18:29:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep +* [Tue Sep 22 03:08:03 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 -* [Mon Aug 18 18:29:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds +* [Tue Sep 22 03:08:03 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.* @@ -13684,8 +13721,8 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. @@ -13827,12 +13864,14 @@ 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/728110/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/728110/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/4072441 and its subdirectories -I: Current time: Mon Aug 18 18:29:22 -12 2025 -I: pbuilder-time-stamp: 1755584962 +I: removing directory /srv/workspace/pbuilder/728110 and its subdirectories +I: Current time: Tue Sep 22 03:08:39 +14 2026 +I: pbuilder-time-stamp: 1789996119