Diff of the two buildlogs: -- --- b1/build.log 2025-02-26 02:53:02.918915576 +0000 +++ b2/build.log 2025-02-26 03:01:45.695382273 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 25 14:46:43 -12 2025 -I: pbuilder-time-stamp: 1740538003 +I: Current time: Tue Mar 31 23:16:05 +14 2026 +I: pbuilder-time-stamp: 1774948565 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1624869/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/128809/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 31 09:16 /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/128809/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/128809/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a341f7e7f5394291ad86dcc1ceafd623' - 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='1624869' - PS1='# ' - PS2='> ' + INVOCATION_ID=de17432a176e44bfba0327b2334d0060 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=128809 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.IyNhoyxa/pbuilderrc_d3DZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IyNhoyxa/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.IyNhoyxa/pbuilderrc_aVjs --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IyNhoyxa/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1624869/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/128809/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -283,7 +315,7 @@ Get: 163 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 130 MB in 1s (130 MB/s) +Fetched 130 MB in 3s (46.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19775 files and directories currently installed.) @@ -837,8 +869,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Feb 26 02:47:33 UTC 2025. -Universal Time is now: Wed Feb 26 02:47:33 UTC 2025. +Local time is now: Tue Mar 31 09:17:03 UTC 2026. +Universal Time is now: Tue Mar 31 09:17:03 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14) ... @@ -988,7 +1020,11 @@ 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/128809/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/128809/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 @@ -1051,7 +1087,7 @@ ## 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 -* [Tue Feb 25 14:47:46 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 Mar 31 23:17:24 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. @@ -1103,13 +1139,13 @@ fi -Building a new DB, current time: 02/25/2025 14:47:46 +Building a new DB, current time: 03/31/2026 23:17:25 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 0.00389099 seconds. +Adding sequences from FASTA; added 240 sequences in 0.0064249 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1185,7 +1221,7 @@ 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: 2409.47 +# Mc/sec: 1567.45 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1242,8 +1278,8 @@ 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: 2462.68 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1531.44 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1307,8 +1343,8 @@ 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 2583.48 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1778.16 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1369,7 +1405,7 @@ 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: 3022.22 +# Mc/sec: 1847.71 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1430,7 +1466,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1097.62 +# Mc/sec: 732.56 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1481,7 +1517,7 @@ 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: 915.81 +# Mc/sec: 634.63 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1546,7 +1582,7 @@ 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: 2701.81 +# Mc/sec: 2050.37 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1598,8 +1634,8 @@ 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: 948.34 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 725.81 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1649,8 +1685,8 @@ 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: 2505.37 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2101.73 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1707,7 +1743,7 @@ 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: 3135.77 +# Mc/sec: 2159.00 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1796,7 +1832,7 @@ 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: 2417.04 +# Mc/sec: 1802.78 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1880,8 +1916,8 @@ 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: 2770.81 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1668.68 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1937,8 +1973,8 @@ 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: 1370.92 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1072.90 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1994,8 +2030,8 @@ 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: 1543.76 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 1156.73 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2052,7 +2088,7 @@ 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: 3811.82 +# Mc/sec: 2477.48 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2096,8 +2132,8 @@ 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: 3231.98 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2361.30 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2150,7 +2186,7 @@ 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: 3907.21 +# Mc/sec: 2602.06 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2195,7 +2231,7 @@ 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: 2299.77 +# Mc/sec: 1618.39 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2255,8 +2291,8 @@ 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: 2031.59 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1511.30 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2306,8 +2342,8 @@ 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: 1807.36 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1157.81 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2419,8 +2455,8 @@ 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: 1504.49 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1158.48 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2467,7 +2503,7 @@ 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: 2794.67 +# Mc/sec: 1954.22 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2534,7 +2570,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2766.15 +# Mc/sec: 2051.47 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2573,7 +2609,7 @@ 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: 4799.92 +# Mc/sec: 3434.99 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2650,7 +2686,7 @@ 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: 2131.11 +# Mc/sec: 1317.10 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2703,7 +2739,7 @@ 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: 3480.37 +# Mc/sec: 2169.73 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2788,7 +2824,7 @@ 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: 00:00:00.00 -# Mc/sec: 762.79 +# Mc/sec: 531.53 // Query: DLH [M=217] Accession: PF01738.17 @@ -2836,7 +2872,7 @@ 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: 4383.85 +# Mc/sec: 2807.68 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2883,7 +2919,7 @@ 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: 2636.64 +# Mc/sec: 1927.37 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2932,8 +2968,8 @@ 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: 3491.65 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2512.08 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2976,7 +3012,7 @@ 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: 3885.61 +# Mc/sec: 2988.35 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3022,7 +3058,7 @@ 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: 1764.66 +# Mc/sec: 1155.45 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3060,7 +3096,7 @@ 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: 4359.99 +# Mc/sec: 3134.34 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3112,7 +3148,7 @@ 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: 2143.46 +# Mc/sec: 1388.94 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3150,7 +3186,7 @@ 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: 2210.75 +# Mc/sec: 1503.70 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3188,7 +3224,7 @@ 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: 3903.78 +# Mc/sec: 2840.73 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3238,8 +3274,8 @@ 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: 2844.93 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2034.09 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3276,8 +3312,8 @@ 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: 5775.26 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4063.03 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3338,7 +3374,7 @@ 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: 3196.29 +# Mc/sec: 2084.56 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3383,7 +3419,7 @@ 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: 3015.06 +# Mc/sec: 2306.97 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3440,7 +3476,7 @@ 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: 3372.40 +# Mc/sec: 2237.47 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3495,7 +3531,7 @@ 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: 1376.43 +# Mc/sec: 1000.12 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3533,7 +3569,7 @@ 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: 4880.62 +# Mc/sec: 3714.13 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3610,7 +3646,7 @@ 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: 3525.05 +# Mc/sec: 2430.13 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3674,8 +3710,8 @@ 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: 1163.81 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 837.10 // Query: FPP [M=866] Accession: PF05911.10 @@ -3725,8 +3761,8 @@ 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: 3227.66 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2057.83 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3779,7 +3815,7 @@ 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: 3012.38 +# Mc/sec: 2222.21 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3902,8 +3938,8 @@ 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: 00:00:00.00 -# Mc/sec: 1000.84 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 669.45 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3942,7 +3978,7 @@ 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: 2231.51 +# Mc/sec: 1636.48 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4033,7 +4069,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1168.55 +# Mc/sec: 901.19 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4083,8 +4119,8 @@ 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: 892.93 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 568.31 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4144,8 +4180,8 @@ 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: 2193.70 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1245.05 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4250,7 +4286,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1281.54 +# Mc/sec: 703.82 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4297,8 +4333,8 @@ 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: 3385.53 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1871.77 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4372,8 +4408,8 @@ 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: 1945.56 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1093.25 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4444,7 +4480,7 @@ 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: 2922.56 +# Mc/sec: 1763.62 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4491,8 +4527,8 @@ 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: 1367.06 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1073.04 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4562,8 +4598,8 @@ 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: 520.00 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 373.72 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4614,7 +4650,7 @@ 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: 3701.75 +# Mc/sec: 3044.00 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4664,8 +4700,8 @@ 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: 4103.20 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 3780.62 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4704,7 +4740,7 @@ 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: 2808.83 +# Mc/sec: 2037.92 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4749,7 +4785,7 @@ 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: 2613.55 +# Mc/sec: 1791.95 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4801,7 +4837,7 @@ 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: 2221.78 +# Mc/sec: 1539.44 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4883,8 +4919,8 @@ 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: 1569.54 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1238.03 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4985,7 +5021,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 1322.26 +# Mc/sec: 929.28 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5039,8 +5075,8 @@ 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: 1852.71 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1522.05 // Query: IBR [M=62] Accession: PF01485.20 @@ -5077,8 +5113,8 @@ 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: 2378.20 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1881.62 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5126,7 +5162,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1623.86 +# Mc/sec: 1370.38 // Query: malic [M=182] Accession: PF00390.18 @@ -5165,7 +5201,7 @@ 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: 4920.85 +# Mc/sec: 4183.42 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5202,8 +5238,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1996.65 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1494.80 // Query: MatE [M=161] Accession: PF01554.17 @@ -5287,8 +5323,8 @@ 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: 2141.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1598.11 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5326,7 +5362,7 @@ 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: 4354.64 +# Mc/sec: 3472.47 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5500,8 +5536,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 378.15 +# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 276.66 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5544,7 +5580,7 @@ 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: 3334.48 +# Mc/sec: 2210.53 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5600,8 +5636,8 @@ 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: 1959.22 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1444.09 // Query: MIP [M=227] Accession: PF00230.19 @@ -5652,7 +5688,7 @@ 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: 2970.44 +# Mc/sec: 2775.17 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5705,7 +5741,7 @@ 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: 2020.31 +# Mc/sec: 1668.94 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5795,8 +5831,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 2829.82 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2595.45 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5833,8 +5869,8 @@ 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: 2660.12 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1972.73 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5872,7 +5908,7 @@ 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: 4549.96 +# Mc/sec: 3562.16 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5925,7 +5961,7 @@ 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: 3420.94 +# Mc/sec: 3150.39 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5963,7 +5999,7 @@ 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: 5096.31 +# Mc/sec: 3692.96 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6083,8 +6119,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 1688.09 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1389.20 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6135,7 +6171,7 @@ 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: 2616.98 +# Mc/sec: 3448.86 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6205,8 +6241,8 @@ 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: 3078.32 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 2856.00 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6258,8 +6294,8 @@ 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: 1618.15 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1353.32 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6322,7 +6358,7 @@ 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: 2320.23 +# Mc/sec: 2024.47 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6424,8 +6460,8 @@ 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: 471.09 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 361.19 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6473,7 +6509,7 @@ 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: 3563.93 +# Mc/sec: 2831.65 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6524,7 +6560,7 @@ 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: 1970.33 +# Mc/sec: 1988.25 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6575,7 +6611,7 @@ 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: 3140.59 +# Mc/sec: 2919.08 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6626,7 +6662,7 @@ 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: 4697.30 +# Mc/sec: 3823.54 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6670,8 +6706,8 @@ 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: 4391.07 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 4200.05 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6718,7 +6754,7 @@ 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: 2022.15 +# Mc/sec: 1848.47 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6782,8 +6818,8 @@ 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: 934.08 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 778.58 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6828,7 +6864,7 @@ 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: 2567.17 +# Mc/sec: 2712.76 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6881,7 +6917,7 @@ 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: 1578.83 +# Mc/sec: 1274.23 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6926,7 +6962,7 @@ 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: 3895.25 +# Mc/sec: 4215.39 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7026,8 +7062,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 917.05 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 +# Mc/sec: 683.72 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7072,7 +7108,7 @@ 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: 1175.82 +# Mc/sec: 978.46 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7124,8 +7160,8 @@ 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: 3021.12 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 3180.24 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7198,8 +7234,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 -# Mc/sec: 715.54 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 543.94 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7260,7 +7296,7 @@ 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: 3014.37 +# Mc/sec: 2252.63 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7305,7 +7341,7 @@ 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: 3003.23 +# Mc/sec: 2482.19 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7358,7 +7394,7 @@ 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: 3200.90 +# Mc/sec: 2470.25 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7396,7 +7432,7 @@ 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: 7312.88 +# Mc/sec: 5582.05 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7439,7 +7475,7 @@ 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: 4040.64 +# Mc/sec: 3375.67 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7501,8 +7537,8 @@ 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: 1276.31 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 +# Mc/sec: 863.18 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7540,7 +7576,7 @@ 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: 4418.26 +# Mc/sec: 3536.34 // Query: Usher [M=551] Accession: PF00577.19 @@ -7585,7 +7621,7 @@ 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: 4250.95 +# Mc/sec: 2926.89 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7632,7 +7668,7 @@ 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: 1196.06 +# Mc/sec: 919.01 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7677,7 +7713,7 @@ 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: 1286.09 +# Mc/sec: 898.57 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7722,7 +7758,7 @@ 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: 1347.56 +# Mc/sec: 909.11 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7777,7 +7813,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1426.38 +# Mc/sec: 974.31 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7816,7 +7852,7 @@ 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: 1024.01 +# Mc/sec: 702.39 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7868,7 +7904,7 @@ 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: 1374.62 +# Mc/sec: 921.54 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7915,8 +7951,8 @@ 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: 2064.01 +# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 +# Mc/sec: 1420.86 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7955,14 +7991,14 @@ 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: 2015.49 +# Mc/sec: 1149.57 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Tue Feb 25 14:47:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Feb 25 14:47:47 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 Mar 31 23:17:27 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 Mar 31 23:17:27 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 @@ -7989,39 +8025,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Tue Feb 25 14:47:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:17:28 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 -* [Tue Feb 25 14:47:47 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 -* [Tue Feb 25 14:47:48 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/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 Feb 25 14:47:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:17:28 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 Mar 31 23:17:28 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 Mar 31 23:17:29 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... -* [Tue Feb 25 14:47:48 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* [Tue Feb 25 14:47:48 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 -* [Tue Feb 25 14:47:48 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 Mar 31 23:17:29 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 Mar 31 23:17:29 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 Mar 31 23:17:29 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 -* [Tue Feb 25 14:48:00 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:17:45 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 -* [Tue Feb 25 14:48:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Mar 31 23:17:50 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 -* [Tue Feb 25 14:48:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Mar 31 23:17:51 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 -* [Tue Feb 25 14:48:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Mar 31 23:17:52 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 -* [Tue Feb 25 14:48:04 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Mar 31 23:17:53 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 -* [Tue Feb 25 14:48:05 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 Mar 31 23:17:53 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 @@ -8031,33 +8067,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Tue Feb 25 14:48:05 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/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 Mar 31 23:17:53 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 -* [Tue Feb 25 14:48:16 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 Mar 31 23:18:09 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 -* [Tue Feb 25 14:48:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Mar 31 23:18:13 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 -* [Tue Feb 25 14:48:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Mar 31 23:18:14 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 -* [Tue Feb 25 14:48:20 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 Mar 31 23:18:15 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 -* [Tue Feb 25 14:48:21 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 Mar 31 23:18:16 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 -* [Tue Feb 25 14:48:21 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* [Tue Feb 25 14:48:21 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 Mar 31 23:18:16 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 Mar 31 23:18:16 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 -* [Tue Feb 25 14:48:21 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 Mar 31 23:18:16 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 -* [Tue Feb 25 14:48:21 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 Mar 31 23:18:16 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.* @@ -8149,7 +8185,7 @@ ../../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 -* [Tue Feb 25 14:48:21 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 Mar 31 23:18:17 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. @@ -8173,8 +8209,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Tue Feb 25 14:48:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Feb 25 14:48:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:18:19 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 Mar 31 23:18:19 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 @@ -8849,37 +8885,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Tue Feb 25 14:48:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:18:20 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 -* [Tue Feb 25 14:48:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Feb 25 14:48:24 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 -* [Tue Feb 25 14:48:28 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/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 Mar 31 23:18:20 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 Mar 31 23:18:21 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 Mar 31 23:18:26 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/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 -* [Tue Feb 25 14:48:28 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* [Tue Feb 25 14:48:28 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 -* [Tue Feb 25 14:48:28 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 Mar 31 23:18:26 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 Mar 31 23:18:26 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 Mar 31 23:18:26 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 -* [Tue Feb 25 14:48:46 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 Mar 31 23:18:47 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 -* [Tue Feb 25 14:48:50 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 Mar 31 23:18:53 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 -* [Tue Feb 25 14:48:51 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 Mar 31 23:18:54 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 -* [Tue Feb 25 14:48:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Mar 31 23:18:55 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 -* [Tue Feb 25 14:48:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Mar 31 23:18:55 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 -* [Tue Feb 25 14:48:53 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 Mar 31 23:18:56 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 @@ -8938,33 +8974,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Tue Feb 25 14:48:53 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 Mar 31 23:18:56 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 -* [Tue Feb 25 14:49:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Mar 31 23:19:16 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 -* [Tue Feb 25 14:49:14 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Mar 31 23:19:22 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 -* [Tue Feb 25 14:49:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Mar 31 23:19:23 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 -* [Tue Feb 25 14:49:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Mar 31 23:19:24 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 -* [Tue Feb 25 14:49:16 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 Mar 31 23:19:25 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 -* [Tue Feb 25 14:49:16 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* [Tue Feb 25 14:49:16 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 Mar 31 23:19:25 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 Mar 31 23:19:25 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 -* [Tue Feb 25 14:49:16 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 Mar 31 23:19:25 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 -* [Tue Feb 25 14:49:16 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 Mar 31 23:19:26 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.* @@ -9057,7 +9093,7 @@ 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 -* [Tue Feb 25 14:49:17 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 Mar 31 23:19:27 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. @@ -9077,8 +9113,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Tue Feb 25 14:49:19 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 -* [Tue Feb 25 14:49:19 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 Mar 31 23:19:29 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 Mar 31 23:19:29 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 @@ -9116,37 +9152,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Tue Feb 25 14:49:19 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 Mar 31 23:19:30 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 -* [Tue Feb 25 14:49:19 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 -* [Tue Feb 25 14:49:21 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 -* [Tue Feb 25 14:49:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 +* [Tue Mar 31 23:19:30 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 Mar 31 23:19:32 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 Mar 31 23:19:37 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 -* [Tue Feb 25 14:49:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Tue Feb 25 14:49:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 -* [Tue Feb 25 14:49:26 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores +* [Tue Mar 31 23:19:37 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 Mar 31 23:19:37 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 Mar 31 23:19:38 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 -* [Tue Feb 25 14:49:45 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 Mar 31 23:20:02 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 -* [Tue Feb 25 14:49:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Mar 31 23:20:08 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 -* [Tue Feb 25 14:49:50 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Mar 31 23:20:09 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 -* [Tue Feb 25 14:49:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Mar 31 23:20:10 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 -* [Tue Feb 25 14:49:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Mar 31 23:20:11 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Tue Feb 25 14:49:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:20:11 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 @@ -9252,33 +9288,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Tue Feb 25 14:49:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores +* [Tue Mar 31 23:20:12 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/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 -* [Tue Feb 25 14:50:09 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 Mar 31 23:20:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Tue Feb 25 14:50:13 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Tue Mar 31 23:20:37 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 -* [Tue Feb 25 14:50:14 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Mar 31 23:20:38 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 -* [Tue Feb 25 14:50:15 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Mar 31 23:20:39 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 -* [Tue Feb 25 14:50:15 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 Mar 31 23:20:40 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 -* [Tue Feb 25 14:50:15 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* [Tue Feb 25 14:50:15 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 Mar 31 23:20:40 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 Mar 31 23:20:40 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 -* [Tue Feb 25 14:50:15 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 Mar 31 23:20:40 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 -* [Tue Feb 25 14:50:16 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 Mar 31 23:20:41 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.* @@ -9297,30 +9333,30 @@ $VAR1 = { 'orient' => '-', 'contig' => 'III', - 'asmbl' => 'comp1051_c1_seq1', - 'trans_id' => '', 'coords' => [ [ '1642973', '1644586' ] ], - 'gene_id' => '' + 'gene_id' => '', + 'asmbl' => 'comp1051_c1_seq1', + 'trans_id' => '' }; - gene_type: protein-coding is_pseudogene: 0 - classification: annotated_genes Model_feat_name: comp1051_c1_seq1.p1 - source: transdecoder + classification: annotated_genes + num_exons: 1 + gene_type: protein-coding mid_pt: 808 - asmbl_id: comp1051_c1_seq1 + source: transdecoder + is_5prime_partial: 0 strand: + - num_exons: 1 + is_3prime_partial: 0 TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 - gene_length: 1616 com_name: ORF type:5prime_partial (+),score=83.26 - is_3prime_partial: 0 - is_5prime_partial: 0 + asmbl_id: comp1051_c1_seq1 + gene_length: 1616 gene_synonyms: mRNA_coords CDS_coords @@ -9337,11 +9373,10 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '-', + 'contig' => 'I', 'asmbl' => 'comp1058_c0_seq1', 'trans_id' => '', - 'contig' => 'I', - 'orient' => '-', - 'gene_id' => '', 'coords' => [ [ 5095548, @@ -9351,22 +9386,23 @@ 5095142, '5095301' ] - ] + ], + 'gene_id' => '' }; - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - gene_length: 496 - com_name: ORF type:5prime_partial (+),score=32.57 - is_3prime_partial: 0 - is_5prime_partial: 0 - classification: annotated_genes Model_feat_name: comp1058_c0_seq1.p1 - gene_type: protein-coding is_pseudogene: 0 - asmbl_id: comp1058_c0_seq1 - mid_pt: 248 - strand: + + gene_type: protein-coding num_exons: 1 + mid_pt: 248 source: transdecoder + classification: annotated_genes + is_5prime_partial: 0 + strand: + + gene_length: 496 + asmbl_id: comp1058_c0_seq1 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=32.57 gene_synonyms: mRNA_coords CDS_coords @@ -9389,6 +9425,8 @@ -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'contig' => 'III', + 'orient' => '-', 'gene_id' => '', 'coords' => [ [ @@ -9401,24 +9439,22 @@ ] ], 'trans_id' => '', - 'asmbl' => 'comp1112_c0_seq1', - 'contig' => 'III', - 'orient' => '-' + 'asmbl' => 'comp1112_c0_seq1' }; - com_name: ORF type:complete (+),score=155.28 + mid_pt: 1041 + source: transdecoder + num_exons: 1 + gene_type: protein-coding + classification: annotated_genes + Model_feat_name: comp1112_c0_seq1.p1 + is_pseudogene: 0 + asmbl_id: comp1112_c0_seq1 gene_length: 2081 + com_name: ORF type:complete (+),score=155.28 TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 - is_5prime_partial: 0 is_3prime_partial: 0 - is_pseudogene: 0 - gene_type: protein-coding - Model_feat_name: comp1112_c0_seq1.p1 - classification: annotated_genes - source: transdecoder - num_exons: 1 + is_5prime_partial: 0 strand: + - mid_pt: 1041 - asmbl_id: comp1112_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9440,10 +9476,9 @@ -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', - 'orient' => '-', - 'asmbl' => 'comp1198_c0_seq1', 'trans_id' => '', + 'asmbl' => 'comp1198_c0_seq1', + 'gene_id' => '', 'coords' => [ [ 402195, @@ -9462,22 +9497,23 @@ '401683' ] ], - 'gene_id' => '' + 'contig' => 'II', + 'orient' => '-' }; + is_3prime_partial: 0 + TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 com_name: ORF type:internal (+),score=37.56 gene_length: 597 - TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 + asmbl_id: comp1198_c0_seq1 + strand: + is_5prime_partial: 0 - is_3prime_partial: 0 - Model_feat_name: comp1198_c0_seq1.p1 classification: annotated_genes - is_pseudogene: 0 gene_type: protein-coding num_exons: 1 - strand: + - mid_pt: 299 - asmbl_id: comp1198_c0_seq1 source: transdecoder + mid_pt: 299 + is_pseudogene: 0 + Model_feat_name: comp1198_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9507,9 +9543,6 @@ $VAR1 = { 'asmbl' => 'comp1210_c0_seq1', 'trans_id' => '', - 'orient' => '-', - 'contig' => 'III', - 'gene_id' => '', 'coords' => [ [ 368840, @@ -9519,22 +9552,25 @@ 367430, '368790' ] - ] + ], + 'gene_id' => '', + 'contig' => 'III', + 'orient' => '-' }; - TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=12.16 - gene_length: 1554 - is_3prime_partial: 0 - is_5prime_partial: 0 - gene_type: protein-coding - is_pseudogene: 0 - Model_feat_name: comp1210_c0_seq1.p1 classification: annotated_genes source: transdecoder mid_pt: 777 - asmbl_id: comp1210_c0_seq1 num_exons: 1 + gene_type: protein-coding + is_pseudogene: 0 + Model_feat_name: comp1210_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=12.16 + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 + is_3prime_partial: 0 + asmbl_id: comp1210_c0_seq1 + gene_length: 1554 strand: + + is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9559,10 +9595,10 @@ -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '-', + 'contig' => 'II', 'trans_id' => '', 'asmbl' => 'comp366_c0_seq1', - 'contig' => 'II', - 'orient' => '-', 'gene_id' => '', 'coords' => [ [ @@ -9571,20 +9607,20 @@ ] ] }; - com_name: ORF type:internal (-),score=12.83 - gene_length: 340 - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 - is_5prime_partial: 0 - is_3prime_partial: 0 - is_pseudogene: 0 - gene_type: protein-coding - Model_feat_name: comp366_c0_seq1.p1 classification: annotated_genes source: transdecoder - num_exons: 1 - strand: - mid_pt: 170 + gene_type: protein-coding + num_exons: 1 + is_pseudogene: 0 + Model_feat_name: comp366_c0_seq1.p1 + com_name: ORF type:internal (-),score=12.83 + is_3prime_partial: 0 + TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + gene_length: 340 asmbl_id: comp366_c0_seq1 + is_5prime_partial: 0 + strand: - gene_synonyms: mRNA_coords CDS_coords @@ -9610,31 +9646,31 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'asmbl' => 'comp610_c0_seq1', - 'trans_id' => '', 'orient' => '-', 'contig' => 'I', - 'gene_id' => '', 'coords' => [ [ '5471264', '5472770' ] - ] + ], + 'gene_id' => '', + 'asmbl' => 'comp610_c0_seq1', + 'trans_id' => '' }; - is_5prime_partial: 0 is_3prime_partial: 0 - gene_length: 1509 - com_name: ORF type:5prime_partial (+),score=50.55 TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - source: transdecoder + com_name: ORF type:5prime_partial (+),score=50.55 + gene_length: 1509 + asmbl_id: comp610_c0_seq1 + is_5prime_partial: 0 strand: + + classification: annotated_genes + gene_type: protein-coding num_exons: 1 + source: transdecoder mid_pt: 755 - asmbl_id: comp610_c0_seq1 is_pseudogene: 0 - gene_type: protein-coding - classification: annotated_genes Model_feat_name: comp610_c0_seq1.p1 gene_synonyms: mRNA_coords @@ -9654,32 +9690,32 @@ -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], + 'gene_id' => '', 'asmbl' => 'comp645_c0_seq1', 'trans_id' => '', - 'contig' => 'I', - 'orient' => '-' + 'orient' => '-', + 'contig' => 'I' }; - num_exons: 1 - strand: + - asmbl_id: comp645_c0_seq1 - mid_pt: 1827 - source: transdecoder + is_pseudogene: 0 Model_feat_name: comp645_c0_seq1.p1 classification: annotated_genes - is_pseudogene: 0 + mid_pt: 1827 + source: transdecoder gene_type: protein-coding + num_exons: 1 + strand: + is_5prime_partial: 0 - is_3prime_partial: 0 com_name: ORF type:5prime_partial (+),score=273.35 - gene_length: 3653 + is_3prime_partial: 0 TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 + gene_length: 3653 + asmbl_id: comp645_c0_seq1 gene_synonyms: mRNA_coords CDS_coords @@ -9697,9 +9733,6 @@ $VAR1 = { 'asmbl' => 'comp688_c0_seq1', 'trans_id' => '', - 'orient' => '+', - 'contig' => 'II', - 'gene_id' => '', 'coords' => [ [ 380308, @@ -9709,22 +9742,25 @@ 380624, '381243' ] - ] + ], + 'gene_id' => '', + 'contig' => 'II', + 'orient' => '+' }; - is_3prime_partial: 0 is_5prime_partial: 0 - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + strand: + + asmbl_id: comp688_c0_seq1 gene_length: 2784 com_name: ORF type:complete (+),score=172.54 + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 + is_3prime_partial: 0 + Model_feat_name: comp688_c0_seq1.p1 + is_pseudogene: 0 + source: transdecoder mid_pt: 1392 - asmbl_id: comp688_c0_seq1 - strand: + num_exons: 1 - source: transdecoder - classification: annotated_genes - Model_feat_name: comp688_c0_seq1.p1 gene_type: protein-coding - is_pseudogene: 0 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9748,6 +9784,8 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', + 'asmbl' => 'comp856_c0_seq1', 'gene_id' => '', 'coords' => [ [ @@ -9759,25 +9797,23 @@ '3755057' ] ], - 'asmbl' => 'comp856_c0_seq1', - 'trans_id' => '', 'contig' => 'II', 'orient' => '+' }; - is_5prime_partial: 0 - is_3prime_partial: 0 - com_name: ORF type:complete (+),score=71.94 - gene_length: 1569 - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + Model_feat_name: comp856_c0_seq1.p1 + is_pseudogene: 0 source: transdecoder - num_exons: 1 - strand: + mid_pt: 785 - asmbl_id: comp856_c0_seq1 - is_pseudogene: 0 gene_type: protein-coding - Model_feat_name: comp856_c0_seq1.p1 + num_exons: 1 classification: annotated_genes + is_5prime_partial: 0 + strand: + + gene_length: 1569 + asmbl_id: comp856_c0_seq1 + com_name: ORF type:complete (+),score=71.94 + is_3prime_partial: 0 + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords @@ -9814,23 +9850,23 @@ ], 'trans_id' => '', 'asmbl' => 'comp873_c0_seq2', - 'contig' => 'II', - 'orient' => '-' + 'orient' => '-', + 'contig' => 'II' }; - com_name: ORF type:5prime_partial (+),score=8.59 - gene_length: 1025 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 is_5prime_partial: 0 + strand: + + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=8.59 + gene_length: 1025 + asmbl_id: comp873_c0_seq2 is_pseudogene: 0 - gene_type: protein-coding Model_feat_name: comp873_c0_seq2.p1 classification: annotated_genes - source: transdecoder + gene_type: protein-coding num_exons: 1 - strand: + + source: transdecoder mid_pt: 513 - asmbl_id: comp873_c0_seq2 gene_synonyms: mRNA_coords CDS_coords @@ -9854,6 +9890,8 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '-', + 'contig' => 'III', 'gene_id' => '', 'coords' => [ [ @@ -9865,25 +9903,23 @@ '1268172' ] ], - 'asmbl' => 'comp888_c0_seq1', 'trans_id' => '', - 'contig' => 'III', - 'orient' => '-' + 'asmbl' => 'comp888_c0_seq1' }; - is_pseudogene: 0 - gene_type: protein-coding - classification: annotated_genes - Model_feat_name: comp888_c0_seq1.p1 - source: transdecoder - strand: + - num_exons: 1 - asmbl_id: comp888_c0_seq1 - mid_pt: 295 gene_length: 589 - com_name: ORF type:5prime_partial (+),score=23.94 + asmbl_id: comp888_c0_seq1 TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 - is_5prime_partial: 0 is_3prime_partial: 0 + com_name: ORF type:5prime_partial (+),score=23.94 + is_5prime_partial: 0 + strand: + + gene_type: protein-coding + num_exons: 1 + mid_pt: 295 + source: transdecoder + classification: annotated_genes + Model_feat_name: comp888_c0_seq1.p1 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9905,6 +9941,8 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'trans_id' => '', + 'asmbl' => 'comp940_c0_seq1', 'gene_id' => '', 'coords' => [ [ @@ -9916,25 +9954,23 @@ '106404' ] ], - 'asmbl' => 'comp940_c0_seq1', - 'trans_id' => '', 'orient' => '+', 'contig' => 'III' }; - Model_feat_name: comp940_c0_seq1.p1 - classification: annotated_genes - is_pseudogene: 0 gene_type: protein-coding num_exons: 1 - strand: + mid_pt: 1065 - asmbl_id: comp940_c0_seq1 source: transdecoder - com_name: ORF type:complete (+),score=94.37 + classification: annotated_genes + Model_feat_name: comp940_c0_seq1.p1 + is_pseudogene: 0 gene_length: 2129 + asmbl_id: comp940_c0_seq1 TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 - is_5prime_partial: 0 is_3prime_partial: 0 + com_name: ORF type:complete (+),score=94.37 + is_5prime_partial: 0 + strand: + gene_synonyms: mRNA_coords CDS_coords @@ -9954,7 +9990,8 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'contig' => 'I', + 'orient' => '-', 'coords' => [ [ 4100066, @@ -9965,25 +10002,24 @@ '4100014' ] ], - 'trans_id' => '', + 'gene_id' => '', 'asmbl' => 'comp983_c0_seq1', - 'orient' => '-', - 'contig' => 'I' + 'trans_id' => '' }; - strand: + + classification: annotated_genes num_exons: 1 - asmbl_id: comp983_c0_seq1 + gene_type: protein-coding mid_pt: 935 source: transdecoder - classification: annotated_genes - Model_feat_name: comp983_c0_seq1.p1 is_pseudogene: 0 - gene_type: protein-coding - is_5prime_partial: 0 + Model_feat_name: comp983_c0_seq1.p1 is_3prime_partial: 0 - gene_length: 1870 - com_name: ORF type:5prime_partial (+),score=143.65 TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 + com_name: ORF type:5prime_partial (+),score=143.65 + asmbl_id: comp983_c0_seq1 + gene_length: 1870 + strand: + + is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -10027,7 +10063,7 @@ ## 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 -* [Tue Feb 25 14:50:17 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 Mar 31 23:20:43 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. @@ -10052,8 +10088,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Tue Feb 25 14:50:26 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 -* [Tue Feb 25 14:50:26 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 Mar 31 23:20:54 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 Mar 31 23:20:55 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 @@ -12671,37 +12707,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Tue Feb 25 14:50:28 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 Mar 31 23:20:57 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 -* [Tue Feb 25 14:50:28 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 -* [Tue Feb 25 14:50:30 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 -* [Tue Feb 25 14:50:54 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 Mar 31 23:20:57 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 Mar 31 23:21:00 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 Mar 31 23:21:30 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Tue Feb 25 14:50:55 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* [Tue Feb 25 14:50:55 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 -* [Tue Feb 25 14:50:56 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/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 Mar 31 23:21:31 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 Mar 31 23:21:31 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 Mar 31 23:21:33 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.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 -* [Tue Feb 25 14:51:15 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 Mar 31 23:21:56 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Tue Feb 25 14:51:19 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Mar 31 23:22:02 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 -* [Tue Feb 25 14:51:20 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Tue Mar 31 23:22:03 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Tue Feb 25 14:51:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Tue Mar 31 23:22:04 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 -* [Tue Feb 25 14:51:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Mar 31 23:22:05 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 -* [Tue Feb 25 14:51:21 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 Mar 31 23:22:05 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 @@ -12804,33 +12840,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Tue Feb 25 14:51:22 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 Mar 31 23:22:06 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 -* [Tue Feb 25 14:51:40 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 Mar 31 23:22:29 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 -* [Tue Feb 25 14:51:44 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 Mar 31 23:22:34 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 -* [Tue Feb 25 14:51:45 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 Mar 31 23:22:35 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.enhanced.feature.scores.roc null device 1 -* [Tue Feb 25 14:51:46 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 Mar 31 23:22:37 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.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Tue Feb 25 14:51:46 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 Mar 31 23:22:38 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 -* [Tue Feb 25 14:51:47 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* [Tue Feb 25 14:51:47 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 Mar 31 23:22:39 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 Mar 31 23:22:39 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 -* [Tue Feb 25 14:51:47 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 Mar 31 23:22:39 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 -* [Tue Feb 25 14:51:49 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 Mar 31 23:22:41 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.* @@ -12942,7 +12978,7 @@ // 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 -* [Tue Feb 25 14:51:54 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 Mar 31 23:22:49 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. @@ -12966,19 +13002,19 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Tue Feb 25 14:51:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Feb 25 14:51:55 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 +* [Tue Mar 31 23:22:51 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 Mar 31 23:22:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr +-skipping training candidate: bdg_i2.p1, not unique enough -skipping training candidate: bdg_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_i2.p1, not unique enough -skipping training candidate: eIF5B_i3.p1, not unique enough +-skipping training candidate: eIF5B_i2.p1, not unique enough -skipping training candidate: 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 @@ -12993,27 +13029,27 @@ -skipping training candidate: Calx_i5.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_i4.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough --skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: CG8312_i4.p1, not unique enough +-skipping training candidate: Klp10A_i5.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_i1.p1, not unique enough +-skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough --skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough +-skipping training candidate: CG6424_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: CG33970_i1.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough -skipping training candidate: CG12581_i1.p1, not unique enough --skipping training candidate: CG6091_i3.p1, not unique enough +-skipping training candidate: CG6091_i1.p1, not unique enough +-skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: hrg_i2.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough --skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough @@ -13025,35 +13061,35 @@ -skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough --skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough +-skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough --skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough +-skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Est-6_i2.p1, not unique enough --skipping training candidate: S-Lap3_i3.p1, not unique enough +-skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: S-Lap3_i1.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough -skipping training candidate: CG30438_i1.p1, not unique enough -skipping training candidate: CG30438_i3.p1, not unique enough --skipping training candidate: CG30438_i5.p1, not unique enough +-skipping training candidate: CG30438_i2.p1, not unique enough -skipping training candidate: 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_i3.p1, not unique enough --skipping training candidate: Eno_i1.p1, not unique enough +-skipping training candidate: Eno_i5.p1, not unique enough +-skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough --skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_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_i10.p1, not unique enough -skipping training candidate: Aldh-III_i8.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough @@ -13061,14 +13097,14 @@ -skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough --skipping training candidate: Eno_i5.p2, not unique enough --skipping training candidate: Eno_i4.p2, not unique enough +-skipping training candidate: Eno_i1.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough --skipping training candidate: Eno_i1.p2, not unique enough --skipping training candidate: CG6424_i3.p2, not unique enough +-skipping training candidate: Eno_i5.p2, not unique enough +-skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: CG6424_i4.p2, not unique enough -skipping training candidate: CG6424_i2.p2, not unique enough +-skipping training candidate: CG6424_i3.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough @@ -13076,8 +13112,8 @@ -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_i3.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: AdipoR_i2.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough -skipping training candidate: Tm1_i5.p1, not unique enough @@ -13087,17 +13123,17 @@ -skipping training candidate: Lip4_i1.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough --skipping training candidate: nmo_i7.p1, not unique enough --skipping training candidate: CG8136_i3.p1, not unique enough +-skipping training candidate: nmo_i1.p1, not unique enough -skipping training candidate: CG8136_i1.p1, not unique enough +-skipping training candidate: CG8136_i3.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough +-skipping training candidate: CG7564_i2.p3, not unique enough -skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG7564_i1.p1, not unique enough --skipping training candidate: CG7564_i3.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough --skipping training candidate: nmo_i5.p1, not unique enough --skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_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: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough @@ -13105,24 +13141,24 @@ -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough --skipping training candidate: ogre_i4.p1, not unique enough --skipping training candidate: ogre_i3.p1, not unique enough --skipping training candidate: ogre_i1.p1, not unique enough --skipping training candidate: ogre_i2.p1, not unique enough -skipping training candidate: ogre_i6.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough +-skipping training candidate: ogre_i2.p1, not unique enough +-skipping training candidate: ogre_i1.p1, not unique enough +-skipping training candidate: ogre_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_i2.p1, not unique enough +-skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough -skipping training candidate: CG13284_i5.p1, not unique enough -skipping training candidate: CG13284_i1.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_i2.p2, not unique enough +-skipping training candidate: Klp10A_i5.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_i1.p2, not unique enough +-skipping training candidate: Klp10A_i3.p2, not unique enough -skipping training candidate: Klp10A_i4.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough @@ -13131,532 +13167,536 @@ -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_i2.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough +-skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough --skipping training candidate: l(3)05822_i1.p2, not unique enough -skipping training candidate: l(3)05822_i4.p2, not unique enough +-skipping training candidate: l(3)05822_i1.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_i6.p1, not unique enough +-skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough --skipping training candidate: Tm1_i3.p1, not unique enough --skipping training candidate: Tm1_i6.p1, not unique enough --skipping training candidate: Npl4_i2.p2, not unique enough +-skipping training candidate: Npl4_i1.p2, not unique enough -skipping training candidate: Npl4_i3.p2, not unique enough +-skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough --skipping training candidate: Sec16_i1.p2, not unique enough --skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough +-skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: Dgk_i1.p2, not unique enough --skipping training candidate: eIF5B_i2.p2, not unique enough --skipping training candidate: eIF5B_i1.p2, not unique enough +-skipping training candidate: eIF5B_i4.p2, not unique enough -skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: eIF5B_i3.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: eIF5B_i2.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough --skipping training candidate: l(1)G0193_i1.p2, not unique enough +-skipping training candidate: Dgk_i3.p2, not unique enough +-skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: l(1)G0193_i2.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough -skipping training candidate: Dgk_i4.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_i2.p3, not unique enough --skipping training candidate: l(3)05822_i1.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: l(3)05822_i4.p3, not unique enough +-skipping training candidate: l(3)05822_i1.p3, not unique enough -skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i2.p2, not unique enough --skipping training candidate: Sec16_i6.p2, not unique enough +-skipping training candidate: Sec16_i5.p3, not unique enough -skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: CG13887_i2.p1, not unique enough --skipping training candidate: CG13887_i1.p1, not unique enough +-skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough +-skipping training candidate: nmo_i5.p2, not unique enough +-skipping training candidate: nmo_i7.p2, not unique enough -skipping training candidate: nmo_i3.p2, not unique enough -skipping training candidate: nmo_i6.p2, not unique enough --skipping training candidate: nmo_i7.p2, not unique enough --skipping training candidate: nmo_i2.p2, not unique enough +-skipping training candidate: nmo_i1.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough --skipping training candidate: gukh_i4.p3, not unique enough +-skipping training candidate: gukh_i1.p2, not unique enough -skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough -skipping training candidate: RpL15_i1.p1, not unique enough --skipping training candidate: RpL15_i2.p1, not unique enough +-skipping training candidate: RpL15_i5.p1, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough +-skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i3.p1, not unique enough --skipping training candidate: RpL15_i5.p1, not unique enough --skipping training candidate: Npl4_i2.p3, not unique enough +-skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: Npl4_i3.p3, not unique enough --skipping training candidate: trc_i1.p2, not unique enough --skipping training candidate: Hsc70-1_i1.p3, not unique enough +-skipping training candidate: trc_i2.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough +-skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough --skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough +-skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough +-skipping training candidate: CG10237_i3.p2, not unique enough -skipping training candidate: CG10237_i2.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough -skipping training candidate: CG10237_i5.p2, not unique enough --skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Eno_i6.p3, not unique enough -skipping training candidate: Eno_i3.p3, not unique enough +-skipping training candidate: Eno_i5.p3, not unique enough +-skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i1.p3, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough --skipping training candidate: Sec16_i1.p3, not unique enough +-skipping training candidate: Sec16_i3.p2, 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: ATPsyn-d_i1.p1, not unique enough --skipping training candidate: CG10082_i1.p2, not unique enough +-skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough --skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough +-skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG30438_i4.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_i5.p2, not unique enough +-skipping training candidate: CG30438_i2.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough --skipping training candidate: cdi_i1.p3, not unique enough --skipping training candidate: CG14995_i4.p3, not unique enough +-skipping training candidate: cdi_i2.p2, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough +-skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i1.p1, not unique enough --skipping training candidate: ADD1_i2.p2, not unique enough +-skipping training candidate: ADD1_i3.p2, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough --skipping training candidate: Sec16_i1.p4, not unique enough --skipping training candidate: bic_i2.p1, not unique enough +-skipping training candidate: Sec16_i3.p3, 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_i3.p1, not unique enough -skipping training candidate: ctp_i2.p1, not unique enough -skipping training candidate: ctp_i4.p1, not unique enough +-skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough --skipping training candidate: Eno_i4.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough -skipping training candidate: Eno_i3.p4, not unique enough +-skipping training candidate: Eno_i5.p4, not unique enough +-skipping training candidate: Eno_i4.p4, not unique enough -skipping training candidate: Eno_i2.p4, not unique enough --skipping training candidate: Eno_i1.p4, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Klp10A_i5.p3, 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_i1.p3, not unique enough +-skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Calx_i3.p2, not unique enough +-skipping training candidate: Calx_i7.p3, not unique enough -skipping training candidate: Calx_i1.p2, not unique enough -skipping training candidate: Calx_i2.p2, not unique enough --skipping training candidate: Calx_i9.p2, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i3.p2, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough +-skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough -skipping training candidate: Calx_i8.p2, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough +-skipping training candidate: CG7564_i2.p5, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough --skipping training candidate: Gale_i2.p2, not unique enough --skipping training candidate: eIF5B_i2.p3, not unique enough --skipping training candidate: eIF5B_i1.p3, not unique enough +-skipping training candidate: Gale_i1.p2, not unique enough +-skipping training candidate: eIF5B_i4.p3, not unique enough -skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: eIF5B_i2.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough --skipping training candidate: AdipoR_i3.p2, not unique enough --skipping training candidate: CG6424_i3.p3, not unique enough --skipping training candidate: CG6424_i3.p4, not unique enough +-skipping training candidate: AdipoR_i4.p2, not unique enough -skipping training candidate: CG6424_i4.p3, not unique enough -skipping training candidate: CG6424_i2.p3, not unique enough --skipping training candidate: Tm1_i16.p2, not unique enough --skipping training candidate: Tm1_i14.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_i13.p2, not unique enough -skipping training candidate: Tm1_i5.p2, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Tm1_i16.p2, not unique enough -skipping training candidate: Dgk_i7.p5, not unique enough --skipping training candidate: Dgk_i2.p5, not unique enough +-skipping training candidate: Dgk_i3.p4, not unique enough +-skipping training candidate: Dgk_i6.p4, not unique enough -skipping training candidate: Dgk_i1.p4, not unique enough --skipping training candidate: cdi_i1.p4, not unique enough --skipping training candidate: eff_i2.p1, not unique enough +-skipping training candidate: cdi_i2.p3, not unique enough +-skipping training candidate: eff_i1.p1, not unique enough -skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i2.p4, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough +-skipping training candidate: eIF5B_i4.p5, not unique enough -skipping training candidate: eIF5B_i5.p4, not unique enough -skipping training candidate: eIF5B_i3.p4, not unique enough --skipping training candidate: Sec16_i3.p4, not unique enough +-skipping training candidate: eIF5B_i2.p4, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough +-skipping training candidate: Sec16_i5.p4, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough --skipping training candidate: Sec16_i1.p5, 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: CG32082_i3.p2, not unique enough --skipping training candidate: CG3530_i3.p2, not unique enough +-skipping training candidate: CG32082_i4.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_i2.p6, not unique enough --skipping training candidate: l(3)05822_i1.p5, not unique enough +-skipping training candidate: Dgk_i7.p6, not unique enough -skipping training candidate: l(3)05822_i4.p4, not unique enough +-skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: sqd_i1.p2, not unique enough +-skipping training candidate: CG7564_i2.p6, not unique enough -skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: CG7564_i1.p4, not unique enough --skipping training candidate: CG7564_i3.p4, not unique enough --skipping training candidate: S-Lap3_i3.p2, not unique enough +-skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough --skipping training candidate: cdi_i1.p5, not unique enough --skipping training candidate: CG6091_i3.p2, not unique enough --skipping training candidate: CG6091_i4.p2, not unique enough +-skipping training candidate: cdi_i2.p4, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough +-skipping training candidate: CG6091_i4.p2, not unique enough +-skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough --skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough -skipping training candidate: Cnx99A_i2.p2, not unique enough --skipping training candidate: Sec16_i3.p5, not unique enough +-skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Sec16_i6.p4, not unique enough --skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: Sec16_i5.p5, not unique enough +-skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: ogre_i6.p2, not unique enough -skipping training candidate: CG6024_i2.p3, not unique enough --skipping training candidate: hrg_i1.p3, not unique enough -skipping training candidate: hrg_i4.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_i3.p3, not unique enough -skipping training candidate: CG6091_i4.p3, not unique enough +-skipping training candidate: CG6091_i1.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: CG33970_i1.p2, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough -skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough --skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: Aldh-III_i8.p2, not unique enough +-skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: CG13284_i2.p2, not unique enough --skipping training candidate: CG13284_i4.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough -skipping training candidate: CG13284_i5.p2, not unique enough +-skipping training candidate: CG13284_i4.p2, not unique enough +-skipping training candidate: Lip4_i3.p2, not unique enough -skipping training candidate: Lip4_i1.p2, not unique enough --skipping training candidate: Lip4_i2.p2, not unique enough --skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough --skipping training candidate: Dgk_i7.p7, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Dgk_i7.p7, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough --skipping training candidate: Tm1_i16.p3, not unique enough --skipping training candidate: Tm1_i14.p3, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough +-skipping training candidate: Dgk_i6.p5, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough +-skipping training candidate: Tm1_i13.p3, not unique enough -skipping training candidate: Tm1_i5.p3, not unique enough --skipping training candidate: CG8312_i3.p3, not unique enough --skipping training candidate: CG8312_i3.p4, not unique enough --skipping training candidate: CG8312_i1.p2, not unique enough --skipping training candidate: CG8312_i1.p3, not unique enough +-skipping training candidate: Tm1_i16.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: Klp10A_i2.p6, not unique enough +-skipping training candidate: CG8312_i4.p3, not unique enough +-skipping training candidate: CG8312_i4.p4, not unique enough +-skipping training candidate: CG8312_i1.p2, not unique enough +-skipping training candidate: CG8312_i1.p3, not unique enough +-skipping training candidate: Klp10A_i5.p4, 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_i1.p4, not unique enough +-skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i4.p4, not unique enough --skipping training candidate: eff_i2.p2, not unique enough +-skipping training candidate: eff_i1.p2, not unique enough -skipping training candidate: eff_i3.p2, not unique enough --skipping training candidate: CG14995_i5.p5, not unique enough +-skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough --skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough --skipping training candidate: CG6424_i3.p5, not unique enough +-skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG6424_i4.p4, not unique enough -skipping training candidate: CG6424_i2.p4, not unique enough +-skipping training candidate: CG6424_i3.p5, not unique enough -skipping training candidate: CG12581_i1.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: CG32082_i3.p3, not unique enough --skipping training candidate: Cnx99A_i1.p3, not unique enough +-skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: Cnx99A_i2.p3, not unique enough +-skipping training candidate: Cnx99A_i3.p3, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough -skipping training candidate: CG33970_i2.p3, not unique enough --skipping training candidate: CG33970_i3.p3, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough +-skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: Sec16_i6.p5, not unique enough +-skipping training candidate: Sec16_i5.p6, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough +-skipping training candidate: Sec16_i3.p6, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough --skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: mge_i3.p1, not unique enough -skipping training candidate: CG6024_i2.p4, not unique enough --skipping training candidate: Myo61F_i4.p2, not unique enough --skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Myo61F_i1.p2, not unique enough +-skipping training candidate: Myo61F_i4.p2, not unique enough +-skipping training candidate: Myo61F_i2.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough --skipping training candidate: Cnx99A_i1.p4, not unique enough -skipping training candidate: Cnx99A_i2.p4, not unique enough +-skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: CG13887_i2.p2, not unique enough --skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough --skipping training candidate: CG6145_i4.p2, not unique enough --skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG6145_i2.p2, not unique enough +-skipping training candidate: CG6145_i5.p2, not unique enough +-skipping training candidate: CG6145_i1.p2, not unique enough +-skipping training candidate: CG6145_i4.p2, not unique enough +-skipping training candidate: Calx_i3.p3, not unique enough +-skipping training candidate: Calx_i7.p5, not unique enough -skipping training candidate: Calx_i1.p3, not unique enough -skipping training candidate: Calx_i2.p3, not unique enough --skipping training candidate: Calx_i9.p3, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i3.p3, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough +-skipping training candidate: Calx_i9.p3, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough -skipping training candidate: Calx_i8.p3, not unique enough --skipping training candidate: mge_i1.p2, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough --skipping training candidate: AdipoR_i3.p3, not unique enough +-skipping training candidate: mge_i2.p2, not unique enough -skipping training candidate: AdipoR_i5.p2, not unique enough +-skipping training candidate: AdipoR_i1.p2, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough --skipping training candidate: Aldh-III_i1.p2, not unique enough +-skipping training candidate: Aldh-III_i4.p2, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough +-skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i7.p2, not unique enough --skipping training candidate: Aldh-III_i4.p2, not unique enough +-skipping training candidate: Aldh-III_i1.p2, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i4.p3, not unique enough +-skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough --skipping training candidate: hrg_i4.p4, not unique enough --skipping training candidate: CG33125_i1.p3, not unique enough +-skipping training candidate: CG33125_i2.p2, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i1.p4, not unique enough --skipping training candidate: Sec16_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_i5.p7, not unique enough +-skipping training candidate: Sec16_i5.p8, not unique enough -skipping training candidate: Sec16_i4.p8, not unique enough -skipping training candidate: Sec16_i4.p9, not unique enough +-skipping training candidate: Sec16_i3.p7, not unique enough +-skipping training candidate: Sec16_i3.p8, not unique enough -skipping training candidate: Sec16_i2.p8, not unique enough -skipping training candidate: Sec16_i2.p9, not unique enough --skipping training candidate: Sec16_i1.p8, not unique enough --skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough --skipping training candidate: CG6091_i3.p4, not unique enough --skipping training candidate: CG6091_i4.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough +-skipping training candidate: CG6091_i4.p4, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CanB2_i1.p2, not unique enough -skipping training candidate: IP3K1_i1.p3, not unique enough --skipping training candidate: Klp10A_i2.p8, not unique enough +-skipping training candidate: Klp10A_i5.p5, 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_i1.p6, not unique enough +-skipping training candidate: Klp10A_i3.p5, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Est-6_i2.p2, not unique enough --skipping training candidate: Klp10A_i2.p9, not unique enough +-skipping training candidate: Klp10A_i5.p6, 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_i1.p7, not unique enough +-skipping training candidate: Klp10A_i3.p6, not unique enough -skipping training candidate: Klp10A_i4.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: ADD1_i3.p4, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough --skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Cnx99A_i2.p5, not unique enough --skipping training candidate: Myo61F_i4.p3, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough +-skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Myo61F_i1.p3, not unique enough --skipping training candidate: Myo61F_i4.p4, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough +-skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Myo61F_i2.p3, not unique enough -skipping training candidate: Myo61F_i1.p4, not unique enough --skipping training candidate: bic_i2.p2, not unique enough --skipping training candidate: CG10082_i1.p5, not unique enough --skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: Myo61F_i4.p4, not unique enough +-skipping training candidate: Myo61F_i2.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_i2.p4, not unique enough -skipping training candidate: CG32082_i3.p4, not unique enough --skipping training candidate: Eno_i4.p6, not unique enough +-skipping training candidate: CG32082_i4.p6, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough -skipping training candidate: Eno_i3.p5, not unique enough +-skipping training candidate: Eno_i5.p6, not unique enough +-skipping training candidate: Eno_i4.p6, not unique enough -skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i1.p6, not unique enough --skipping training candidate: Sec16_i3.p9, not unique enough --skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough --skipping training candidate: Dgk_i6.p6, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough --skipping training candidate: Dgk_i7.p8, not unique enough +-skipping training candidate: Sec16_i4.p10, not unique enough +-skipping training candidate: Sec16_i3.p9, not unique enough -skipping training candidate: Dgk_i2.p8, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough +-skipping training candidate: Dgk_i7.p8, not unique enough -skipping training candidate: Dgk_i5.p5, not unique enough +-skipping training candidate: Dgk_i3.p6, not unique enough +-skipping training candidate: Dgk_i6.p6, not unique enough +-skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: nmo_i6.p3, not unique enough --skipping training candidate: CG33970_i2.p5, not unique enough --skipping training candidate: sqd_i3.p2, not unique enough --skipping training candidate: Dgk_i3.p7, not unique enough +-skipping training candidate: CG33970_i1.p4, not unique enough +-skipping training candidate: sqd_i5.p3, 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_i1.p1, not unique enough --skipping training candidate: His4r_i3.p1, not unique enough --skipping training candidate: Hsc70-1_i1.p4, not unique enough +-skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough --skipping training candidate: hrg_i1.p5, not unique enough +-skipping training candidate: Hsc70-1_i1.p4, not unique enough -skipping training candidate: hrg_i4.p6, not unique enough +-skipping training candidate: hrg_i1.p5, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough -skipping training candidate: CG8136_i3.p2, not unique enough --skipping training candidate: CG8136_i1.p2, not unique enough --skipping training candidate: Myo61F_i4.p5, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: Myo61F_i1.p5, not unique enough --skipping training candidate: CG6091_i3.p5, not unique enough --skipping training candidate: CG6091_i4.p5, not unique enough +-skipping training candidate: Myo61F_i4.p5, not unique enough +-skipping training candidate: Myo61F_i2.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough --skipping training candidate: CG6145_i4.p3, not unique enough --skipping training candidate: CG6145_i5.p3, not unique enough +-skipping training candidate: CG6091_i4.p5, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6145_i2.p3, not unique enough +-skipping training candidate: CG6145_i5.p3, not unique enough +-skipping training candidate: CG6145_i1.p3, not unique enough +-skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: gukh_i1.p4, not unique enough --skipping training candidate: sqd_i3.p3, not unique enough --skipping training candidate: CG33125_i1.p4, not unique enough +-skipping training candidate: sqd_i5.p4, not unique enough +-skipping training candidate: CG33125_i2.p3, not unique enough -skipping training candidate: gukh_i1.p5, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Tue Feb 25 14:51:56 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 Mar 31 23:22:52 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 -* [Tue Feb 25 14:51:56 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 -* [Tue Feb 25 14:51:56 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 -* [Tue Feb 25 14:52:00 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/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 Mar 31 23:22:52 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 Mar 31 23:22:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 Mar 31 23:22:57 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 -* [Tue Feb 25 14:52:00 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* [Tue Feb 25 14:52:00 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 -* [Tue Feb 25 14:52:00 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 Mar 31 23:22:57 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 Mar 31 23:22:57 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 Mar 31 23:22:58 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 -* [Tue Feb 25 14:52:18 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 Mar 31 23:23:22 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/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 -* [Tue Feb 25 14:52:23 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Tue Mar 31 23:23:28 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Tue Feb 25 14:52:23 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 Mar 31 23:23:30 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 -* [Tue Feb 25 14:52:24 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 Mar 31 23:23:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Tue Feb 25 14:52:25 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Tue Mar 31 23:23:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Tue Feb 25 14:52:25 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 Mar 31 23:23:32 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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: -1.00543514671565 instead of -3.40142662700844 --feature swap of score: -1.46432148596605 instead of -3.14785415847568 --feature swap of score: -1.9037779032724 instead of -2.66240859704931 --feature swap of score: -1.23277519768341 instead of -1.94193870650035 --feature swap of score: -0.791226696948313 instead of -1.57824854552847 --feature swap of score: -0.732230972257386 instead of -1.02431680206065 --feature swap of score: 1.90188912636426 instead of -1.00314171949191 --feature swap of score: -0.563314812862065 instead of -1.36442871603328 --feature swap of score: 2.5973746684396 instead of -1.04119218020584 --feature swap of score: -0.616486623153309 instead of -2.47786029066494 --feature swap of score: 2.49398368938698 instead of -1.4340127358657 --feature swap of score: -1.32657116573588 instead of -1.38423428715037 --feature swap of score: -0.599440442330032 instead of -1.16969419870603 --feature swap of score: -0.0904346729809148 instead of -1.29562665813388 --feature swap of score: 1.27225577085655 instead of -0.877277573891095 --feature swap of score: 1.9554762021251 instead of -1.1295226402907 --feature swap of score: -0.996459128729341 instead of -1.26437121647906 --feature swap of score: -0.114100711195927 instead of -1.22686441813161 --feature swap of score: -0.317437469784515 instead of -1.39713098878006 --feature swap of score: 0.289199400372387 instead of -0.706613842658656 --feature swap of score: -0.0445967169823297 instead of -0.565980740950253 --feature swap of score: 0.161779045372927 instead of -0.526505541070503 --feature swap of score: 3.55456453050844 instead of -0.731179168128221 --feature swap of score: 0.829352006608259 instead of -0.907048662872257 --feature swap of score: -0.449772450480797 instead of -0.675555988787786 --feature swap of score: 3.20946261366009 instead of -1.04821022980234 --feature swap of score: -0.320972572957933 instead of -0.782455923828697 --feature swap of score: -0.0158344845267542 instead of -0.512326936302486 --feature swap of score: 1.23400787820259 instead of -0.305990008331877 --feature swap of score: 2.00031357094175 instead of 0.180709509390428 --feature swap of score: 2.11178909073042 instead of -0.0256840405883218 --feature swap of score: 0.274584496533231 instead of 0.0755174016192407 --feature swap of score: 0.584404933163247 instead of -0.135348040794951 --feature swap of score: 0.897308856929456 instead of -0.253859228174635 --feature swap of score: 0.013941772767302 instead of -0.172009755877327 --feature swap of score: 1.09839541814663 instead of -0.514398598544996 --feature swap of score: 3.38601061284181 instead of -0.147443954534029 --feature swap of score: 0.598566684650634 instead of -0.0389436278873752 --feature swap of score: 1.72750200468185 instead of 0.012405748634612 --feature swap of score: 0.823931866091526 instead of -0.255121261320382 --feature swap of score: 0.339991527431866 instead of -0.346458436419504 --feature swap of score: 1.72658890207231 instead of -0.475883912529805 --feature swap of score: -0.0209331140785217 instead of -0.357155231821697 --feature swap of score: 1.81256762626362 instead of -0.113984778764312 --feature swap of score: 1.37129895530782 instead of 0.328941293788467 --feature swap of score: 0.507666215256196 instead of 0.106934390570108 --feature swap of score: 3.90239805108127 instead of -0.0315534387796575 --feature swap of score: 1.29970562072695 instead of -0.133247446249 --feature swap of score: 2.91214919538302 instead of -0.530274781744055 --feature swap of score: 0.0817773279429721 instead of -0.566515609505656 --feature swap of score: 1.57461894471321 instead of 0.0898903517483559 --feature swap of score: 1.76998628329178 instead of -0.0353144855575952 --feature swap of score: 4.80611360029836 instead of 0.499766974540682 --feature swap of score: 1.86563757095963 instead of -0.0178660222481524 --feature swap of score: 6.34424461597118 instead of 0.710554335538014 --feature swap of score: 2.66429813354818 instead of 0.54837240060914 --num feature swaps: 56 -* [Tue Feb 25 14:52:25 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: -1.03130303634808 instead of -3.44414916317431 +-feature swap of score: -1.57345318457767 instead of -3.30864322586671 +-feature swap of score: -1.87379386580513 instead of -2.81334957710587 +-feature swap of score: -1.33446823565114 instead of -1.69632883115065 +-feature swap of score: -0.686820652679612 instead of -1.57871965487136 +-feature swap of score: -0.790741241569552 instead of -1.30493718449466 +-feature swap of score: 2.08965557914986 instead of -1.29429236985983 +-feature swap of score: -0.471762543099697 instead of -1.11655330407987 +-feature swap of score: 2.80010863988867 instead of -1.01187652767108 +-feature swap of score: -0.513293068535892 instead of -2.45191982922666 +-feature swap of score: 2.51295102582455 instead of -1.19983081662128 +-feature swap of score: -1.08134654192534 instead of -1.3408148648572 +-feature swap of score: -0.916128238284676 instead of -1.52661121359494 +-feature swap of score: 0.159328848020455 instead of -1.16642436951984 +-feature swap of score: 1.61794095770487 instead of -1.04112211752569 +-feature swap of score: 2.02598084833262 instead of -1.22594311071454 +-feature swap of score: -1.10868437308696 instead of -1.37036320041102 +-feature swap of score: -0.300602035329592 instead of -1.1835190399235 +-feature swap of score: -0.612924819438146 instead of -1.38002373101882 +-feature swap of score: -0.0430262806050296 instead of -0.956635392638292 +-feature swap of score: 0.0562531667001446 instead of -0.900297029137786 +-feature swap of score: 0.675643346665438 instead of -0.733868483597182 +-feature swap of score: 3.5530101692417 instead of -0.527187220476812 +-feature swap of score: 1.03999173496967 instead of -0.903802266428051 +-feature swap of score: -0.611558202937993 instead of -0.903137200460643 +-feature swap of score: 2.56927226233127 instead of -0.746299894149891 +-feature swap of score: 0.117819772556801 instead of -0.759533915384836 +-feature swap of score: 0.0570925406353685 instead of 0.0271234067949299 +-feature swap of score: 1.69093421486507 instead of -0.110509426116412 +-feature swap of score: 1.34801210019837 instead of 0.0129529961228319 +-feature swap of score: 0.101077552905214 instead of -0.10464231790975 +-feature swap of score: 3.64620107034968 instead of -0.00582241596130606 +-feature swap of score: 0.0223096612322399 instead of -0.0945277172476804 +-feature swap of score: 1.12226636128553 instead of -0.239107698708832 +-feature swap of score: 0.868592314666145 instead of -0.454725849828443 +-feature swap of score: 0.903020679449337 instead of -0.538988144503343 +-feature swap of score: 0.428652259750107 instead of -0.839060253566684 +-feature swap of score: -0.108280352489701 instead of -0.731851787448078 +-feature swap of score: -0.484315465719146 instead of -0.921064743987825 +-feature swap of score: 0.383473996458666 instead of -0.789441437814133 +-feature swap of score: 1.51157486304307 instead of -1.65205336235649 +-feature swap of score: 2.15009127126675 instead of -0.345142364416179 +-feature swap of score: 0.09528105459529 instead of -0.225948228266778 +-feature swap of score: 2.07279122890367 instead of -0.00523520581078163 +-feature swap of score: -0.125131346734113 instead of -0.22501284443086 +-feature swap of score: 0.304985573396165 instead of -0.21023747820915 +-feature swap of score: -0.243243287653774 instead of -0.244873843181093 +-feature swap of score: -0.0876249847291873 instead of -0.35316138199997 +-feature swap of score: 1.71461919300114 instead of 0.299136977337785 +-feature swap of score: 0.669847592039363 instead of -0.0949475718385248 +-feature swap of score: 0.531593305142809 instead of 0.279130557505439 +-feature swap of score: 4.09882197388565 instead of 0.543572968168324 +-feature swap of score: 0.932163185896375 instead of 0.403155291684813 +-feature swap of score: 2.12229003060062 instead of 0.436304708237503 +-feature swap of score: 1.10577893452087 instead of 0.794300119558177 +-feature swap of score: 1.39280655252653 instead of 0.678226890745606 +-feature swap of score: 6.90208614730422 instead of 0.604098789992231 +-feature swap of score: 1.28611390894761 instead of 0.495525435080332 +-feature swap of score: 8.06025455226986 instead of 0.578499038438679 +-feature swap of score: 2.89403110042096 instead of 0.375678113073776 +-num feature swaps: 60 +* [Tue Mar 31 23:23:32 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 -* [Tue Feb 25 14:52:42 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.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 Mar 31 23:23:55 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 -* [Tue Feb 25 14:52:46 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 Mar 31 23:24:02 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 -* [Tue Feb 25 14:52:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Tue Mar 31 23:24:04 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 -* [Tue Feb 25 14:52:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Tue Mar 31 23:24:05 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 -* [Tue Feb 25 14:52:48 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/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 Mar 31 23:24:06 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: 15 -* [Tue Feb 25 14:52:48 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* [Tue Feb 25 14:52:48 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/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed +-number of revised start positions: 14 +* [Tue Mar 31 23:24:06 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 Mar 31 23:24:06 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 -* [Tue Feb 25 14:52:48 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/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 Mar 31 23:24:06 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 -* [Tue Feb 25 14:52:49 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 Mar 31 23:24:07 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.* @@ -13672,9 +13712,9 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. @@ -13806,8 +13846,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-deb: building package 'transdecoder' in '../transdecoder_5.7.1-2_all.deb'. +dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../transdecoder_5.7.1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../transdecoder_5.7.1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13815,12 +13855,14 @@ 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/128809/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/128809/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/1624869 and its subdirectories -I: Current time: Tue Feb 25 14:53:02 -12 2025 -I: pbuilder-time-stamp: 1740538382 +I: removing directory /srv/workspace/pbuilder/128809 and its subdirectories +I: Current time: Tue Mar 31 23:24:44 +14 2026 +I: pbuilder-time-stamp: 1774949084