Diff of the two buildlogs: -- --- b1/build.log 2025-03-08 13:14:01.471791198 +0000 +++ b2/build.log 2025-03-08 13:32:14.534390850 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 10 07:26:57 -12 2026 -I: pbuilder-time-stamp: 1775849217 +I: Current time: Sun Mar 9 03:14:04 +14 2025 +I: pbuilder-time-stamp: 1741439644 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,54 +27,86 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/123159/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/34036/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 8 13:14 /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/34036/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/34036/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='d5dd7a18846f4dd8bc9a97267591d6db' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='123159' - PS1='# ' - PS2='> ' + INVOCATION_ID=819542f3a1344c5c9e0a2b48d79e2756 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=34036 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.GUKVUO8i/pbuilderrc_2zgE --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.GUKVUO8i/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GUKVUO8i/pbuilderrc_Onqn --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.GUKVUO8i/b2 --logfile b2/build.log transdecoder_5.7.1-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/123159/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/34036/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -287,7 +319,7 @@ Get: 163 http://deb.debian.org/debian unstable/main i386 r-cran-tibble i386 3.2.1+dfsg-3 [425 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] -Fetched 132 MB in 2s (54.7 MB/s) +Fetched 132 MB in 1s (91.5 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19769 files and directories currently installed.) @@ -841,8 +873,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 10 19:27:28 UTC 2026. -Universal Time is now: Fri Apr 10 19:27:28 UTC 2026. +Local time is now: Sat Mar 8 13:14:43 UTC 2025. +Universal Time is now: Sat Mar 8 13:14:43 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14) ... @@ -992,7 +1024,11 @@ 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/34036/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/34036/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 @@ -1014,7 +1050,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test - make -j22 test + make -j10 test make[2]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' @@ -1055,7 +1091,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir -* [Fri Apr 10 07:27:40 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 +* [Sun Mar 9 03:15:02 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 -first extracting base frequencies, we'll need them later. @@ -1107,13 +1143,13 @@ fi -Building a new DB, current time: 04/10/2026 07:27:40 +Building a new DB, current time: 03/09/2025 03:15:02 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 0.011618 seconds. +Adding sequences from FASTA; added 240 sequences in 0.013833 seconds. Warning: [blastp] Examining 5 or more matches is recommended @@ -1188,8 +1224,8 @@ 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: 1508.76 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 843.84 // Query: AA_permease_2 [M=425] Accession: PF13520.5 @@ -1246,8 +1282,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1577.72 +# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.01 +# Mc/sec: 803.53 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 @@ -1312,7 +1348,7 @@ 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: 1753.05 +# Mc/sec: 1109.80 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 @@ -1373,7 +1409,7 @@ 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: 1558.53 +# Mc/sec: 1025.45 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 @@ -1433,8 +1469,8 @@ 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: 701.88 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 393.75 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 @@ -1484,8 +1520,8 @@ 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: 405.36 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 286.22 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 @@ -1550,7 +1586,7 @@ 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: 1725.91 +# Mc/sec: 1157.33 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 @@ -1602,8 +1638,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 631.35 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 336.55 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 @@ -1654,7 +1690,7 @@ 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: 1763.94 +# Mc/sec: 1088.80 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 @@ -1710,8 +1746,8 @@ 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: 1779.15 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1039.92 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 @@ -1799,8 +1835,8 @@ 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: 1338.43 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 713.98 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 @@ -1884,8 +1920,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1601.23 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 866.21 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 @@ -1941,8 +1977,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 1002.43 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 542.68 // Query: Aminotran_5 [M=371] Accession: PF00266.18 @@ -1998,8 +2034,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 714.53 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 471.45 // Query: Arginase [M=280] Accession: PF00491.20 @@ -2056,7 +2092,7 @@ 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: 1940.95 +# Mc/sec: 1115.97 // Query: Asparaginase [M=191] Accession: PF00710.19 @@ -2101,7 +2137,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1842.55 +# Mc/sec: 1124.49 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 @@ -2154,7 +2190,7 @@ 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: 2499.74 +# Mc/sec: 1606.10 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 @@ -2198,8 +2234,8 @@ 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: 1583.53 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 992.11 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 @@ -2259,8 +2295,8 @@ 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: 1263.56 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 688.87 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 @@ -2311,7 +2347,7 @@ 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: 1271.14 +# Mc/sec: 755.41 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 @@ -2423,8 +2459,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 1107.52 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 597.37 // Query: CO_dh [M=168] Accession: PF02552.15 @@ -2471,7 +2507,7 @@ 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: 1954.59 +# Mc/sec: 1192.19 // Query: CRCB [M=95] Accession: PF02537.14 @@ -2538,7 +2574,7 @@ 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: 1682.69 +# Mc/sec: 995.44 // Query: CTP_transf_like [M=143] Accession: PF01467.25 @@ -2577,7 +2613,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2847.21 +# Mc/sec: 1858.99 // Query: Dak1 [M=307] Accession: PF02733.16 @@ -2653,8 +2689,8 @@ 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 0.02s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1353.16 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 738.30 // Query: Dak2 [M=174] Accession: PF02734.16 @@ -2707,7 +2743,7 @@ 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: 1794.46 +# Mc/sec: 1041.21 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 @@ -2791,8 +2827,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 460.72 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 269.97 // Query: DLH [M=217] Accession: PF01738.17 @@ -2840,7 +2876,7 @@ 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: 2165.68 +# Mc/sec: 1319.07 // Query: DsrD [M=64] Accession: PF08679.10 @@ -2886,8 +2922,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1746.38 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1006.56 // Query: DUF1129 [M=206] Accession: PF06570.10 @@ -2937,7 +2973,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 2078.07 +# Mc/sec: 1238.56 // Query: DUF1989 [M=167] Accession: PF09347.9 @@ -2979,8 +3015,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 2193.02 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1226.19 // Query: DUF2157 [M=147] Accession: PF09925.8 @@ -3026,7 +3062,7 @@ 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: 791.93 +# Mc/sec: 627.10 // Query: DUF2868 [M=328] Accession: PF11067.7 @@ -3063,8 +3099,8 @@ 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: 2637.24 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1636.50 // Query: DUF2976 [M=88] Accession: PF11190.7 @@ -3116,7 +3152,7 @@ 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: 1387.49 +# Mc/sec: 819.20 // Query: DUF2997 [M=47] Accession: PF11211.7 @@ -3154,7 +3190,7 @@ 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: 1526.94 +# Mc/sec: 859.25 // Query: DUF3288 [M=89] Accession: PF11691.7 @@ -3192,7 +3228,7 @@ 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: 2608.81 +# Mc/sec: 1595.45 // Query: DUF4208 [M=96] Accession: PF13907.5 @@ -3243,7 +3279,7 @@ 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: 1937.51 +# Mc/sec: 1128.73 // Query: DUF705 [M=304] Accession: PF05152.11 @@ -3281,7 +3317,7 @@ 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: 3080.59 +# Mc/sec: 1812.53 // Query: DUF999 [M=143] Accession: PF06198.10 @@ -3342,7 +3378,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1748.15 +# Mc/sec: 1055.41 // Query: FAD_syn [M=158] Accession: PF06574.11 @@ -3387,7 +3423,7 @@ 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: 2004.81 +# Mc/sec: 1259.00 // Query: Fe-ADH [M=364] Accession: PF00465.18 @@ -3443,8 +3479,8 @@ 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: 1727.08 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 896.56 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 @@ -3498,8 +3534,8 @@ 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: 803.71 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 440.53 // Query: Fig1 [M=188] Accession: PF12351.7 @@ -3537,7 +3573,7 @@ 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: 2722.99 +# Mc/sec: 1670.45 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 @@ -3613,8 +3649,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1866.66 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 1185.81 // Query: FMN_red [M=155] Accession: PF03358.14 @@ -3678,8 +3714,8 @@ 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: 738.71 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 396.26 // Query: FPP [M=866] Accession: PF05911.10 @@ -3729,8 +3765,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2023.29 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 1143.68 // Query: FR47 [M=86] Accession: PF08445.9 @@ -3783,7 +3819,7 @@ 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: 2148.20 +# Mc/sec: 1236.26 // Query: Fungal_trans [M=267] Accession: PF04082.17 @@ -3906,8 +3942,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 579.01 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 366.49 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 @@ -3946,7 +3982,7 @@ 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: 1602.11 +# Mc/sec: 917.04 // Query: GDC-P [M=430] Accession: PF02347.15 @@ -4036,8 +4072,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 855.81 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 +# Mc/sec: 438.25 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 @@ -4088,7 +4124,7 @@ 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: 574.03 +# Mc/sec: 306.57 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 @@ -4149,7 +4185,7 @@ 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: 1459.34 +# Mc/sec: 842.61 // Query: GLEYA [M=91] Accession: PF10528.8 @@ -4253,8 +4289,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 839.24 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 485.25 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 @@ -4302,7 +4338,7 @@ 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: 2055.88 +# Mc/sec: 1110.90 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 @@ -4376,8 +4412,8 @@ 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: 1226.15 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 742.66 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 @@ -4447,8 +4483,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1466.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 887.36 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 @@ -4495,8 +4531,8 @@ 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: 899.71 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 525.06 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 @@ -4566,8 +4602,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 344.23 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 +# Mc/sec: 192.05 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 @@ -4617,8 +4653,8 @@ 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: 2551.01 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1570.36 // Query: His_Phos_1 [M=194] Accession: PF00300.21 @@ -4669,7 +4705,7 @@ 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: 2228.01 +# Mc/sec: 1470.03 // Query: Hpt [M=85] Accession: PF01627.22 @@ -4708,7 +4744,7 @@ 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: 2001.95 +# Mc/sec: 1253.78 // Query: HTH_29 [M=63] Accession: PF13551.5 @@ -4753,7 +4789,7 @@ 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: 1846.63 +# Mc/sec: 1078.73 // Query: HTH_psq [M=45] Accession: PF05225.15 @@ -4805,7 +4841,7 @@ 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: 1464.45 +# Mc/sec: 832.41 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 @@ -4887,8 +4923,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1068.62 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 637.65 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 @@ -4988,8 +5024,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 -# Mc/sec: 905.95 +# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 459.67 // Query: Hydant_A_N [M=178] Accession: PF05378.12 @@ -5044,7 +5080,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1322.77 +# Mc/sec: 763.67 // Query: IBR [M=62] Accession: PF01485.20 @@ -5082,7 +5118,7 @@ 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: 1693.34 +# Mc/sec: 980.67 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 @@ -5129,8 +5165,8 @@ 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: 976.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 574.53 // Query: malic [M=182] Accession: PF00390.18 @@ -5168,8 +5204,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 3057.00 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1891.37 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 @@ -5206,8 +5242,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1172.46 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 653.04 // Query: MatE [M=161] Accession: PF01554.17 @@ -5291,8 +5327,8 @@ 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: 1243.14 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 671.44 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 @@ -5329,8 +5365,8 @@ 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: 2727.63 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1557.10 // Query: MFS_1 [M=353] Accession: PF07690.15 @@ -5504,8 +5540,8 @@ Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] -# CPU time: 0.04u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 -# Mc/sec: 265.62 +# CPU time: 0.08u 0.00s 00:00:00.08 Elapsed: 00:00:00.07 +# Mc/sec: 138.29 // Query: MFS_3 [M=522] Accession: PF05977.12 @@ -5547,8 +5583,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 2195.49 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 1267.61 // Query: MFS_4 [M=363] Accession: PF06779.13 @@ -5605,7 +5641,7 @@ 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: 00:00:00.01 -# Mc/sec: 896.63 +# Mc/sec: 696.02 // Query: MIP [M=227] Accession: PF00230.19 @@ -5655,8 +5691,8 @@ 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: 1864.20 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1117.57 // Query: MVP_shoulder [M=118] Accession: PF11978.7 @@ -5708,8 +5744,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1432.22 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 830.39 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 @@ -5799,8 +5835,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 1705.00 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 +# Mc/sec: 878.72 // Query: NEMO [M=68] Accession: PF11577.7 @@ -5837,8 +5873,8 @@ 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: 1817.26 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1049.82 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 @@ -5876,7 +5912,7 @@ 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: 2398.17 +# Mc/sec: 1528.76 // Query: Oleosin [M=113] Accession: PF01277.16 @@ -5929,7 +5965,7 @@ 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: 2153.40 +# Mc/sec: 1295.37 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 @@ -5967,7 +6003,7 @@ 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: 2854.58 +# Mc/sec: 1839.26 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 @@ -6087,8 +6123,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 1086.18 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 559.58 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 @@ -6139,7 +6175,7 @@ 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: 1920.34 +# Mc/sec: 1081.29 // Query: Pantoate_transf [M=259] Accession: PF02548.14 @@ -6209,8 +6245,8 @@ 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: 1669.52 +# CPU time: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 962.87 // Query: Phosphodiest [M=357] Accession: PF01663.21 @@ -6263,7 +6299,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 1018.01 +# Mc/sec: 570.20 // Query: PLA2_B [M=491] Accession: PF01735.17 @@ -6325,8 +6361,8 @@ 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: 1569.44 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 792.93 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 @@ -6428,8 +6464,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 297.27 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 156.07 // Query: Pombe_5TM [M=256] Accession: PF09437.9 @@ -6477,7 +6513,7 @@ 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: 2060.20 +# Mc/sec: 1256.51 // Query: PsbN [M=43] Accession: PF02468.14 @@ -6527,8 +6563,8 @@ 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: 1391.39 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 791.36 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 @@ -6579,7 +6615,7 @@ 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: 1930.79 +# Mc/sec: 1159.09 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 @@ -6630,7 +6666,7 @@ 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: 2018.33 +# Mc/sec: 1239.37 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 @@ -6675,7 +6711,7 @@ 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: 2228.90 +# Mc/sec: 1386.36 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 @@ -6722,7 +6758,7 @@ 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: 1371.88 +# Mc/sec: 802.17 // Query: SAUGI [M=111] Accession: PF06106.10 @@ -6786,8 +6822,8 @@ 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: 575.72 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 298.14 // Query: Smim3 [M=60] Accession: PF17307.1 @@ -6832,7 +6868,7 @@ 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: 1862.16 +# Mc/sec: 1029.01 // Query: SnoaL [M=126] Accession: PF07366.11 @@ -6884,8 +6920,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 916.95 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 514.16 // Query: SnoaL_2 [M=102] Accession: PF12680.6 @@ -6930,7 +6966,7 @@ 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: 2315.29 +# Mc/sec: 1465.91 // Query: Sugar_tr [M=452] Accession: PF00083.23 @@ -7030,8 +7066,8 @@ Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 714.77 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 +# Mc/sec: 353.58 // Query: SUI1 [M=76] Accession: PF01253.21 @@ -7076,7 +7112,7 @@ 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: 473.30 +# Mc/sec: 427.27 // Query: Sulfatase [M=309] Accession: PF00884.22 @@ -7128,8 +7164,8 @@ 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: 2160.52 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1365.66 // Query: ThiJ_like [M=196] Accession: PF17124.4 @@ -7202,8 +7238,8 @@ Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 360.33 +# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02 +# Mc/sec: 247.10 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 @@ -7264,7 +7300,7 @@ 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: 1748.95 +# Mc/sec: 1120.73 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 @@ -7309,7 +7345,7 @@ 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: 1912.34 +# Mc/sec: 1199.02 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 @@ -7361,8 +7397,8 @@ 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: 1878.88 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 +# Mc/sec: 1154.15 // Query: Transferase [M=434] Accession: PF02458.14 @@ -7399,8 +7435,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 3680.59 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 2178.11 // Query: TRAPP [M=146] Accession: PF04051.15 @@ -7443,7 +7479,7 @@ 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: 2277.23 +# Mc/sec: 1338.80 // Query: TRI12 [M=599] Accession: PF06609.12 @@ -7505,8 +7541,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02 -# Mc/sec: 640.94 +# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 +# Mc/sec: 441.41 // Query: UPF0489 [M=178] Accession: PF12640.6 @@ -7544,7 +7580,7 @@ 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: 2819.42 +# Mc/sec: 1780.76 // Query: Usher [M=551] Accession: PF00577.19 @@ -7588,8 +7624,8 @@ 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: 2599.28 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 1566.34 // Query: zf-C2H2 [M=23] Accession: PF00096.25 @@ -7636,7 +7672,7 @@ 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: 846.47 +# Mc/sec: 488.14 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 @@ -7681,7 +7717,7 @@ 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: 821.00 +# Mc/sec: 450.76 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 @@ -7726,7 +7762,7 @@ Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 871.58 +# Mc/sec: 483.06 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 @@ -7781,7 +7817,7 @@ 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: 1000.48 +# Mc/sec: 594.29 // Query: zf-Di19 [M=54] Accession: PF05605.11 @@ -7819,8 +7855,8 @@ Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.00 -# Mc/sec: 548.85 +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 334.94 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 @@ -7872,7 +7908,7 @@ 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: 886.06 +# Mc/sec: 504.77 // Query: zf-TRAF [M=60] Accession: PF02176.17 @@ -7920,7 +7956,7 @@ 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: 1476.46 +# Mc/sec: 823.97 // Query: Zn_clus [M=40] Accession: PF00172.17 @@ -7959,14 +7995,14 @@ 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: 1218.92 +# Mc/sec: 715.30 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v -* [Fri Apr 10 07:27:42 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 -* [Fri Apr 10 07:27:42 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 +* [Sun Mar 9 03:15:05 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 +* [Sun Mar 9 03:15:05 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 -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 @@ -7993,39 +8029,39 @@ -redundancy-minimized set includes 72 / 95 = 75.79% -* [Fri Apr 10 07:27:42 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 +* [Sun Mar 9 03:15:06 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 PCT_GC: 37 -* [Fri Apr 10 07:27:42 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 -* [Fri Apr 10 07:27:43 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 -* [Fri Apr 10 07:27:43 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:15:06 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 +* [Sun Mar 9 03:15:06 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 +* [Sun Mar 9 03:15:08 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 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... -* [Fri Apr 10 07:27:43 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement -Training start codon pattern recognition* [Fri Apr 10 07:27:43 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 -* [Fri Apr 10 07:27:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:15:08 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* [Sun Mar 9 03:15:08 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 +* [Sun Mar 9 03:15:08 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:28:06 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 +* [Sun Mar 9 03:15:49 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 -parsing scores -* [Fri Apr 10 07:28:11 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 || : +* [Sun Mar 9 03:15:57 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 || : null device 1 -* [Fri Apr 10 07:28:12 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 +* [Sun Mar 9 03:15:59 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 null device 1 -* [Fri Apr 10 07:28:13 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sun Mar 9 03:16:01 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:28:14 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : +* [Sun Mar 9 03:16:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:28:14 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:16:03 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 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 @@ -8035,33 +8071,33 @@ -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 -* [Fri Apr 10 07:28:15 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:16:03 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:28:37 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 +* [Sun Mar 9 03:16:41 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Apr 10 07:28:42 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 || : +* [Sun Mar 9 03:16:49 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:28:43 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 +* [Sun Mar 9 03:16:51 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Apr 10 07:28:44 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sun Mar 9 03:16:53 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 || : Loading required package: grid null device 1 -* [Fri Apr 10 07:28:45 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 +* [Sun Mar 9 03:16:53 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 Refining start codon selections. -number of revised start positions: 1 -* [Fri Apr 10 07:28:45 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* [Fri Apr 10 07:28:45 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 +* [Sun Mar 9 03:16:54 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* [Sun Mar 9 03:16:54 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed -* [Fri Apr 10 07:28:45 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 +* [Sun Mar 9 03:16:54 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep -* [Fri Apr 10 07:28:45 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 +* [Sun Mar 9 03:16:54 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 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.* @@ -8153,7 +8189,7 @@ ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir -* [Fri Apr 10 07:28:46 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 +* [Sun Mar 9 03:16:55 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 -first extracting base frequencies, we'll need them later. @@ -8177,8 +8213,8 @@ ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir -* [Fri Apr 10 07:28:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Apr 10 07:28:49 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:16:59 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 +* [Sun Mar 9 03:16:59 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 -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 @@ -8853,37 +8889,37 @@ -redundancy-minimized set includes 396 / 1067 = 37.11% -* [Fri Apr 10 07:28:49 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 +* [Sun Mar 9 03:17:00 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 PCT_GC: 42 -* [Fri Apr 10 07:28:49 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 -* [Fri Apr 10 07:28:50 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 -* [Fri Apr 10 07:28:58 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 +* [Sun Mar 9 03:17:00 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 +* [Sun Mar 9 03:17:02 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 +* [Sun Mar 9 03:17:14 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 Selecting best orfs -* [Fri Apr 10 07:28:58 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* [Fri Apr 10 07:28:58 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 -* [Fri Apr 10 07:28:58 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/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 +* [Sun Mar 9 03:17:15 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* [Sun Mar 9 03:17:15 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 +* [Sun Mar 9 03:17:15 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:29:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:18:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Apr 10 07:29:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : +* [Sun Mar 9 03:18:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:29:40 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc +* [Sun Mar 9 03:18:35 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Apr 10 07:29:41 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sun Mar 9 03:18:37 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 || : Loading required package: grid null device 1 -* [Fri Apr 10 07:29:42 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 || : +* [Sun Mar 9 03:18:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:29:42 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced +* [Sun Mar 9 03:18:39 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -8942,33 +8978,33 @@ -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 -* [Fri Apr 10 07:29:43 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 +* [Sun Mar 9 03:18:39 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:30:15 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 +* [Sun Mar 9 03:19:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Apr 10 07:30:22 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 || : +* [Sun Mar 9 03:19:57 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 || : null device 1 -* [Fri Apr 10 07:30:24 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 +* [Sun Mar 9 03:19:58 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 null device 1 -* [Fri Apr 10 07:30:25 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 || : +* [Sun Mar 9 03:20:00 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 || : Loading required package: grid null device 1 -* [Fri Apr 10 07:30:25 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 +* [Sun Mar 9 03:20:01 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 Refining start codon selections. -number of revised start positions: 83 -* [Fri Apr 10 07:30:26 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* [Fri Apr 10 07:30:26 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 +* [Sun Mar 9 03:20:02 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* [Sun Mar 9 03:20:02 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed -* [Fri Apr 10 07:30:26 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep +* [Sun Mar 9 03:20:02 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep -* [Fri Apr 10 07:30:26 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 +* [Sun Mar 9 03:20:03 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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.* @@ -8989,8 +9025,8 @@ -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. --Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. --Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. +-Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. +-Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 107, 466 @@ -9061,7 +9097,7 @@ make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir -* [Fri Apr 10 07:30:27 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 +* [Sun Mar 9 03:20:05 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 -first extracting base frequencies, we'll need them later. @@ -9081,8 +9117,8 @@ Then, run TransDecoder.Predict for your final coding region predictions. -* [Fri Apr 10 07:30:30 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 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Apr 10 07:30:30 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 +* [Sun Mar 9 03:20:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 +* [Sun Mar 9 03:20:09 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -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 @@ -9120,37 +9156,37 @@ -redundancy-minimized set includes 810 / 844 = 95.97% -* [Fri Apr 10 07:30:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:20:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 -* [Fri Apr 10 07:30:31 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores -* [Fri Apr 10 07:30:33 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 -* [Fri Apr 10 07:30:40 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 +* [Sun Mar 9 03:20:10 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores +* [Sun Mar 9 03:20:14 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 +* [Sun Mar 9 03:20:26 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 Selecting best orfs -* [Fri Apr 10 07:30:40 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* [Fri Apr 10 07:30:40 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 -* [Fri Apr 10 07:30:41 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:20:27 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* [Sun Mar 9 03:20:27 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 +* [Sun Mar 9 03:20:28 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/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:31:16 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/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 +* [Sun Mar 9 03:21:30 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 -parsing scores -* [Fri Apr 10 07:31:24 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 || : +* [Sun Mar 9 03:21:44 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:31:25 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 +* [Sun Mar 9 03:21:45 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Apr 10 07:31:26 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : +* [Sun Mar 9 03:21:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:31:27 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 || : +* [Sun Mar 9 03:21:48 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:31:27 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:21:49 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 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 @@ -9256,33 +9292,33 @@ -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 -* [Fri Apr 10 07:31:28 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 +* [Sun Mar 9 03:21:50 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:32:01 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 +* [Sun Mar 9 03:22:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Apr 10 07:32:08 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.enhanced.feature.scores.roc || : +* [Sun Mar 9 03:23:07 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:32:09 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.enhanced.feature.scores.roc +* [Sun Mar 9 03:23:09 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 null device 1 -* [Fri Apr 10 07:32:10 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.enhanced.+.pwm || : +* [Sun Mar 9 03:23:11 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 || : Loading required package: grid null device 1 -* [Fri Apr 10 07:32:11 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 +* [Sun Mar 9 03:23:12 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 Refining start codon selections. -number of revised start positions: 43 -* [Fri Apr 10 07:32:11 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* [Fri Apr 10 07:32:11 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 +* [Sun Mar 9 03:23:12 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* [Sun Mar 9 03:23:12 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 Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed -* [Fri Apr 10 07:32:11 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep +* [Sun Mar 9 03:23:12 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep -* [Fri Apr 10 07:32:12 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 +* [Sun Mar 9 03:23:13 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 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.* @@ -9299,8 +9335,8 @@ CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'asmbl' => 'comp1051_c1_seq1', 'contig' => 'III', - 'trans_id' => '', 'orient' => '-', 'coords' => [ [ @@ -9308,23 +9344,23 @@ '1644586' ] ], - 'asmbl' => 'comp1051_c1_seq1', + 'trans_id' => '', 'gene_id' => '' }; - gene_type: protein-coding - num_exons: 1 - strand: + gene_length: 1616 - is_pseudogene: 0 - is_5prime_partial: 0 - Model_feat_name: comp1051_c1_seq1.p1 - asmbl_id: comp1051_c1_seq1 - classification: annotated_genes source: transdecoder + is_3prime_partial: 0 + strand: + + gene_type: protein-coding mid_pt: 808 + classification: annotated_genes com_name: ORF type:5prime_partial (+),score=83.26 - is_3prime_partial: 0 + num_exons: 1 TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 + asmbl_id: comp1051_c1_seq1 + Model_feat_name: comp1051_c1_seq1.p1 + is_5prime_partial: 0 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9341,9 +9377,6 @@ -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'I', - 'trans_id' => '', - 'orient' => '-', 'gene_id' => '', 'coords' => [ [ @@ -9355,22 +9388,25 @@ '5095301' ] ], + 'trans_id' => '', + 'contig' => 'I', + 'orient' => '-', 'asmbl' => 'comp1058_c0_seq1' }; - classification: annotated_genes - source: transdecoder - com_name: ORF type:5prime_partial (+),score=32.57 - TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 - is_3prime_partial: 0 - mid_pt: 248 - is_pseudogene: 0 + gene_type: protein-coding strand: + + is_3prime_partial: 0 + source: transdecoder gene_length: 496 - num_exons: 1 - gene_type: protein-coding + is_pseudogene: 0 asmbl_id: comp1058_c0_seq1 - Model_feat_name: comp1058_c0_seq1.p1 is_5prime_partial: 0 + Model_feat_name: comp1058_c0_seq1.p1 + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 + num_exons: 1 + com_name: ORF type:5prime_partial (+),score=32.57 + mid_pt: 248 + classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords @@ -9393,10 +9429,7 @@ -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' => '-', 'trans_id' => '', - 'asmbl' => 'comp1112_c0_seq1', 'coords' => [ [ 2380416, @@ -9407,21 +9440,24 @@ '2380336' ] ], - 'gene_id' => '' + 'gene_id' => '', + 'asmbl' => 'comp1112_c0_seq1', + 'contig' => 'III', + 'orient' => '-' }; + gene_length: 2081 + source: transdecoder is_3prime_partial: 0 - TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 - com_name: ORF type:complete (+),score=155.28 + strand: + + gene_type: protein-coding mid_pt: 1041 - source: transdecoder classification: annotated_genes + com_name: ORF type:complete (+),score=155.28 + num_exons: 1 + TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 + asmbl_id: comp1112_c0_seq1 Model_feat_name: comp1112_c0_seq1.p1 is_5prime_partial: 0 - asmbl_id: comp1112_c0_seq1 - gene_length: 2081 - strand: + - gene_type: protein-coding - num_exons: 1 is_pseudogene: 0 gene_synonyms: mRNA_coords @@ -9444,11 +9480,6 @@ -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' => '-', - 'trans_id' => '', - 'gene_id' => '', - 'asmbl' => 'comp1198_c0_seq1', 'coords' => [ [ 402195, @@ -9466,22 +9497,27 @@ 401352, '401683' ] - ] + ], + 'trans_id' => '', + 'gene_id' => '', + 'asmbl' => 'comp1198_c0_seq1', + 'orient' => '-', + 'contig' => 'II' }; + gene_length: 597 + is_3prime_partial: 0 + source: transdecoder + strand: + + gene_type: protein-coding + com_name: ORF type:internal (+),score=37.56 + classification: annotated_genes + mid_pt: 299 + num_exons: 1 is_5prime_partial: 0 Model_feat_name: comp1198_c0_seq1.p1 asmbl_id: comp1198_c0_seq1 - num_exons: 1 - gene_type: protein-coding - strand: + - gene_length: 597 - is_pseudogene: 0 - mid_pt: 299 - com_name: ORF type:internal (+),score=37.56 TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 - is_3prime_partial: 0 - classification: annotated_genes - source: transdecoder + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9509,10 +9545,6 @@ ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'orient' => '-', - 'trans_id' => '', - 'contig' => 'III', - 'asmbl' => 'comp1210_c0_seq1', 'coords' => [ [ 368840, @@ -9523,21 +9555,25 @@ '368790' ] ], - 'gene_id' => '' + 'trans_id' => '', + 'gene_id' => '', + 'asmbl' => 'comp1210_c0_seq1', + 'orient' => '-', + 'contig' => 'III' }; + is_3prime_partial: 0 + source: transdecoder + gene_length: 1554 gene_type: protein-coding - num_exons: 1 strand: + - gene_length: 1554 + num_exons: 1 + com_name: ORF type:5prime_partial (+),score=12.16 + mid_pt: 777 + classification: annotated_genes is_pseudogene: 0 + asmbl_id: comp1210_c0_seq1 is_5prime_partial: 0 Model_feat_name: comp1210_c0_seq1.p1 - asmbl_id: comp1210_c0_seq1 - classification: annotated_genes - source: transdecoder - mid_pt: 777 - com_name: ORF type:5prime_partial (+),score=12.16 - is_3prime_partial: 0 TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 gene_synonyms: mRNA_coords @@ -9563,9 +9599,6 @@ -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 = { - 'contig' => 'II', - 'trans_id' => '', - 'orient' => '-', 'gene_id' => '', 'coords' => [ [ @@ -9573,22 +9606,25 @@ '3841303' ] ], + 'trans_id' => '', + 'orient' => '-', + 'contig' => 'II', 'asmbl' => 'comp366_c0_seq1' }; - is_5prime_partial: 0 - Model_feat_name: comp366_c0_seq1.p1 - asmbl_id: comp366_c0_seq1 gene_type: protein-coding - num_exons: 1 - gene_length: 340 strand: - - is_pseudogene: 0 - mid_pt: 170 + source: transdecoder is_3prime_partial: 0 + gene_length: 340 + is_pseudogene: 0 + Model_feat_name: comp366_c0_seq1.p1 + is_5prime_partial: 0 + asmbl_id: comp366_c0_seq1 TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 + num_exons: 1 com_name: ORF type:internal (-),score=12.83 - source: transdecoder classification: annotated_genes + mid_pt: 170 gene_synonyms: mRNA_coords CDS_coords @@ -9614,32 +9650,32 @@ -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ '5471264', '5472770' ] ], + 'gene_id' => '', 'asmbl' => 'comp610_c0_seq1', 'contig' => 'I', - 'trans_id' => '', 'orient' => '-' }; - com_name: ORF type:5prime_partial (+),score=50.55 - is_3prime_partial: 0 - TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 - mid_pt: 755 - classification: annotated_genes source: transdecoder - Model_feat_name: comp610_c0_seq1.p1 - is_5prime_partial: 0 - asmbl_id: comp610_c0_seq1 - strand: + + is_3prime_partial: 0 gene_length: 1509 gene_type: protein-coding + strand: + num_exons: 1 + mid_pt: 755 + classification: annotated_genes + com_name: ORF type:5prime_partial (+),score=50.55 is_pseudogene: 0 + TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 + asmbl_id: comp610_c0_seq1 + Model_feat_name: comp610_c0_seq1.p1 + is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9658,32 +9694,32 @@ -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 = { - 'trans_id' => '', - 'orient' => '-', - 'contig' => 'I', - 'gene_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], - 'asmbl' => 'comp645_c0_seq1' + 'trans_id' => '', + 'gene_id' => '', + 'asmbl' => 'comp645_c0_seq1', + 'contig' => 'I', + 'orient' => '-' }; + com_name: ORF type:5prime_partial (+),score=273.35 + mid_pt: 1827 + classification: annotated_genes + num_exons: 1 asmbl_id: comp645_c0_seq1 is_5prime_partial: 0 Model_feat_name: comp645_c0_seq1.p1 + TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 is_pseudogene: 0 - num_exons: 1 - gene_type: protein-coding - strand: + gene_length: 3653 - mid_pt: 1827 - com_name: ORF type:5prime_partial (+),score=273.35 - TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 - is_3prime_partial: 0 - classification: annotated_genes source: transdecoder + is_3prime_partial: 0 + strand: + + gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords @@ -9699,7 +9735,11 @@ ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { + 'orient' => '+', + 'contig' => 'II', 'asmbl' => 'comp688_c0_seq1', + 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 380308, @@ -9709,26 +9749,22 @@ 380624, '381243' ] - ], - 'gene_id' => '', - 'orient' => '+', - 'trans_id' => '', - 'contig' => 'II' + ] }; - is_5prime_partial: 0 + TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 Model_feat_name: comp688_c0_seq1.p1 + is_5prime_partial: 0 asmbl_id: comp688_c0_seq1 - num_exons: 1 - gene_type: protein-coding - strand: + - gene_length: 2784 is_pseudogene: 0 + classification: annotated_genes mid_pt: 1392 com_name: ORF type:complete (+),score=172.54 - TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 - is_3prime_partial: 0 - classification: annotated_genes + num_exons: 1 + strand: + + gene_type: protein-coding + gene_length: 2784 source: transdecoder + is_3prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9752,11 +9788,8 @@ -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'II', - 'orient' => '+', - 'trans_id' => '', 'gene_id' => '', - 'asmbl' => 'comp856_c0_seq1', + 'trans_id' => '', 'coords' => [ [ 3753910, @@ -9766,22 +9799,25 @@ 3754438, '3755057' ] - ] + ], + 'contig' => 'II', + 'orient' => '+', + 'asmbl' => 'comp856_c0_seq1' }; - Model_feat_name: comp856_c0_seq1.p1 - is_5prime_partial: 0 - asmbl_id: comp856_c0_seq1 - strand: + gene_length: 1569 - gene_type: protein-coding - num_exons: 1 - is_pseudogene: 0 - com_name: ORF type:complete (+),score=71.94 + source: transdecoder is_3prime_partial: 0 - TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + strand: + + gene_type: protein-coding mid_pt: 785 classification: annotated_genes - source: transdecoder + com_name: ORF type:complete (+),score=71.94 + num_exons: 1 + TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 + asmbl_id: comp856_c0_seq1 + is_5prime_partial: 0 + Model_feat_name: comp856_c0_seq1.p1 + is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords @@ -9801,9 +9837,8 @@ ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { + 'gene_id' => '', 'trans_id' => '', - 'orient' => '-', - 'contig' => 'II', 'coords' => [ [ 3727877, @@ -9818,23 +9853,24 @@ '3727657' ] ], - 'asmbl' => 'comp873_c0_seq2', - 'gene_id' => '' + 'contig' => 'II', + 'orient' => '-', + 'asmbl' => 'comp873_c0_seq2' }; is_pseudogene: 0 - strand: + - gene_length: 1025 - num_exons: 1 - gene_type: protein-coding + TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 asmbl_id: comp873_c0_seq2 - Model_feat_name: comp873_c0_seq2.p1 is_5prime_partial: 0 + Model_feat_name: comp873_c0_seq2.p1 + num_exons: 1 + mid_pt: 513 classification: annotated_genes - source: transdecoder com_name: ORF type:5prime_partial (+),score=8.59 - TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 + gene_type: protein-coding + strand: + + source: transdecoder is_3prime_partial: 0 - mid_pt: 513 + gene_length: 1025 gene_synonyms: mRNA_coords CDS_coords @@ -9858,10 +9894,11 @@ ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'III', - 'trans_id' => '', 'orient' => '-', + 'contig' => 'III', + 'asmbl' => 'comp888_c0_seq1', 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 1268244, @@ -9871,23 +9908,22 @@ 1267938, '1268172' ] - ], - 'asmbl' => 'comp888_c0_seq1' + ] }; is_pseudogene: 0 + asmbl_id: comp888_c0_seq1 + Model_feat_name: comp888_c0_seq1.p1 + is_5prime_partial: 0 + TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 num_exons: 1 + com_name: ORF type:5prime_partial (+),score=23.94 + mid_pt: 295 + classification: annotated_genes gene_type: protein-coding - gene_length: 589 strand: + - asmbl_id: comp888_c0_seq1 - is_5prime_partial: 0 - Model_feat_name: comp888_c0_seq1.p1 source: transdecoder - classification: annotated_genes - mid_pt: 295 - TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 is_3prime_partial: 0 - com_name: ORF type:5prime_partial (+),score=23.94 + gene_length: 589 gene_synonyms: mRNA_coords CDS_coords @@ -9909,10 +9945,11 @@ -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'trans_id' => '', - 'orient' => '+', 'contig' => 'III', + 'orient' => '+', + 'asmbl' => 'comp940_c0_seq1', 'gene_id' => '', + 'trans_id' => '', 'coords' => [ [ 105641, @@ -9922,23 +9959,22 @@ 105785, '106404' ] - ], - 'asmbl' => 'comp940_c0_seq1' + ] }; - strand: + - gene_length: 2129 - gene_type: protein-coding - num_exons: 1 - is_pseudogene: 0 + asmbl_id: comp940_c0_seq1 Model_feat_name: comp940_c0_seq1.p1 is_5prime_partial: 0 - asmbl_id: comp940_c0_seq1 + TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 + is_pseudogene: 0 + com_name: ORF type:complete (+),score=94.37 + mid_pt: 1065 classification: annotated_genes + num_exons: 1 + strand: + + gene_type: protein-coding + gene_length: 2129 source: transdecoder - com_name: ORF type:complete (+),score=94.37 is_3prime_partial: 0 - TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 - mid_pt: 1065 gene_synonyms: mRNA_coords CDS_coords @@ -9958,9 +9994,9 @@ ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { - 'contig' => 'I', - 'trans_id' => '', + 'asmbl' => 'comp983_c0_seq1', 'orient' => '-', + 'contig' => 'I', 'coords' => [ [ 4100066, @@ -9971,23 +10007,23 @@ '4100014' ] ], - 'asmbl' => 'comp983_c0_seq1', + 'trans_id' => '', 'gene_id' => '' }; + strand: + + gene_type: protein-coding + gene_length: 1870 + is_3prime_partial: 0 + source: transdecoder + TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 asmbl_id: comp983_c0_seq1 is_5prime_partial: 0 Model_feat_name: comp983_c0_seq1.p1 is_pseudogene: 0 - gene_type: protein-coding - num_exons: 1 - gene_length: 1870 - strand: + mid_pt: 935 - is_3prime_partial: 0 - TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 - com_name: ORF type:5prime_partial (+),score=143.65 - source: transdecoder classification: annotated_genes + com_name: ORF type:5prime_partial (+),score=143.65 + num_exons: 1 gene_synonyms: mRNA_coords CDS_coords @@ -10031,7 +10067,7 @@ ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir -* [Fri Apr 10 07:32:14 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 +* [Sun Mar 9 03:23:17 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 -first extracting base frequencies, we'll need them later. @@ -10056,8 +10092,8 @@ ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS -* [Fri Apr 10 07:32:29 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/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -* [Fri Apr 10 07:32:30 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 +* [Sun Mar 9 03:23:42 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 +* [Sun Mar 9 03:23:43 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -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 @@ -12675,37 +12711,37 @@ -redundancy-minimized set includes 1645 / 4259 = 38.62% -* [Fri Apr 10 07:32:32 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 +* [Sun Mar 9 03:23:47 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 -* [Fri Apr 10 07:32:33 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 -* [Fri Apr 10 07:32:36 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 -* [Fri Apr 10 07:33:16 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:23:47 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/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 +* [Sun Mar 9 03:23:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:25:04 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 Selecting best orfs -* [Fri Apr 10 07:33:17 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* [Fri Apr 10 07:33:17 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 -* [Fri Apr 10 07:33:18 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 +* [Sun Mar 9 03:25:05 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* [Sun Mar 9 03:25:05 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 +* [Sun Mar 9 03:25:08 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:33:53 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 +* [Sun Mar 9 03:26:14 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 -parsing scores -* [Fri Apr 10 07:34:02 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 || : +* [Sun Mar 9 03:26:28 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:34:03 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 +* [Sun Mar 9 03:26:30 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 -* [Fri Apr 10 07:34:04 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 || : +* [Sun Mar 9 03:26:32 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:34:05 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 || : +* [Sun Mar 9 03:26:33 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:34:05 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 +* [Sun Mar 9 03:26:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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 @@ -12808,33 +12844,33 @@ -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 -* [Fri Apr 10 07:34:06 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 +* [Sun Mar 9 03:26:35 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:34:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:27:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Apr 10 07:34:46 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 || : +* [Sun Mar 9 03:27:51 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 || : null device 1 -* [Fri Apr 10 07:34:47 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 +* [Sun Mar 9 03:27:53 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Apr 10 07:34:48 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sun Mar 9 03:27:55 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:34:49 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 +* [Sun Mar 9 03:27:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 -* [Fri Apr 10 07:34:51 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* [Fri Apr 10 07:34:51 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 +* [Sun Mar 9 03:27:58 2025] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 +copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Sun Mar 9 03:27:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed -* [Fri Apr 10 07:34:51 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep +* [Sun Mar 9 03:27:59 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep -* [Fri Apr 10 07:34:53 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:28:02 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 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.* @@ -12946,7 +12982,7 @@ // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir -* [Fri Apr 10 07:35:02 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 +* [Sun Mar 9 03:28:17 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 -first extracting base frequencies, we'll need them later. @@ -12970,58 +13006,58 @@ + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta -* [Fri Apr 10 07:35:04 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 -* [Fri Apr 10 07:35:04 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/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 +* [Sun Mar 9 03:28:21 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 +* [Sun Mar 9 03:28:21 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: bdg_i4.p1, not unique enough --skipping training candidate: bdg_i2.p1, not unique enough +-skipping training candidate: bdg_i3.p1, not unique enough -skipping training candidate: bdg_i1.p1, not unique enough -skipping training candidate: Dgk_i7.p1, not unique enough -skipping training candidate: Cdep_i1.p1, not unique enough --skipping training candidate: eIF5B_i2.p1, not unique enough -skipping training candidate: eIF5B_i4.p1, not unique enough +-skipping training candidate: eIF5B_i3.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough --skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: Dgk_i3.p1, not unique enough +-skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough --skipping training candidate: mGluR_i4.p1, not unique enough +-skipping training candidate: mGluR_i3.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough +-skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i5.p1, not unique enough -skipping training candidate: Calx_i4.p1, not unique enough --skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough --skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough --skipping training candidate: Klp10A_i5.p1, not unique enough --skipping training candidate: Klp10A_i4.p1, not unique enough +-skipping training candidate: CG8312_i2.p1, not unique enough +-skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: Klp10A_i3.p1, not unique enough -skipping training candidate: Klp10A_i1.p1, not unique enough -skipping training candidate: Klp10A_i6.p1, not unique enough --skipping training candidate: Klp10A_i2.p1, not unique enough +-skipping training candidate: Klp10A_i4.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough --skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough +-skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: Dgk_i4.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: CG12581_i2.p1, not unique enough -skipping training candidate: CG6091_i3.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: hrg_i2.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough --skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough +-skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough @@ -13029,8 +13065,8 @@ -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_i9.p1, not unique enough @@ -13038,70 +13074,70 @@ -skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough --skipping training candidate: Est-6_i1.p1, not unique enough +-skipping training candidate: Est-6_i2.p1, not unique enough -skipping training candidate: S-Lap3_i2.p1, not unique enough -skipping training candidate: S-Lap3_i1.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough --skipping training candidate: CG30438_i5.p1, not unique enough --skipping training candidate: CG30438_i3.p1, not unique enough -skipping training candidate: CG30438_i1.p1, not unique enough +-skipping training candidate: CG30438_i2.p1, not unique enough +-skipping training candidate: CG30438_i3.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: CG6091_i2.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_i8.p1, not unique enough +-skipping training candidate: Aldh-III_i6.p1, not unique enough +-skipping training candidate: Aldh-III_i3.p1, not unique enough +-skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough +-skipping training candidate: Aldh-III_i8.p1, not unique enough +-skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough --skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough --skipping training candidate: Eno_i6.p1, not unique enough +-skipping training candidate: Eno_i1.p2, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: Eno_i3.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_i5.p2, not unique enough -skipping training candidate: CG6424_i2.p2, not unique enough --skipping training candidate: CG6424_i4.p2, not unique enough -skipping training candidate: CG6424_i1.p2, not unique enough +-skipping training candidate: CG6424_i4.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough --skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Irk2_i4.p1, not unique enough +-skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough +-skipping training candidate: AdipoR_i3.p1, not unique enough -skipping training candidate: AdipoR_i2.p1, not unique enough -skipping training candidate: AdipoR_i5.p1, not unique enough --skipping training candidate: AdipoR_i4.p1, not unique enough --skipping training candidate: Tm1_i14.p1, not unique enough -skipping training candidate: Tm1_i5.p1, not unique enough +-skipping training candidate: Tm1_i14.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough -skipping training candidate: kto_i1.p2, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough -skipping training candidate: nmo_i7.p1, not unique enough --skipping training candidate: nmo_i1.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough +-skipping training candidate: nmo_i3.p1, not unique enough -skipping training candidate: 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_i3.p1, not unique enough +-skipping training candidate: CG7564_i4.p1, not unique enough +-skipping training candidate: CG7564_i1.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough +-skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i5.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough --skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough @@ -13109,557 +13145,562 @@ -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_i3.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_i6.p1, not unique enough +-skipping training candidate: ogre_i3.p1, not unique enough -skipping training candidate: ogre_i4.p1, not unique enough +-skipping training candidate: ogre_i1.p1, not unique enough +-skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough -skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough --skipping training candidate: CG13284_i3.p1, not unique enough +-skipping training candidate: CG13284_i5.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough -skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough --skipping training candidate: Klp10A_i5.p2, not unique enough --skipping training candidate: Klp10A_i4.p2, not unique enough +-skipping training candidate: Klp10A_i2.p2, not unique enough +-skipping training candidate: Klp10A_i3.p2, not unique enough -skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Klp10A_i6.p2, not unique enough --skipping training candidate: Klp10A_i2.p2, not unique enough +-skipping training candidate: Klp10A_i4.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough --skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough +-skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough +-skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i4.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough --skipping training candidate: regucalcin_i2.p1, not unique enough --skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough +-skipping training candidate: CG10237_i3.p1, 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: l(3)05822_i3.p2, not unique enough --skipping training candidate: l(3)05822_i4.p2, not unique enough +-skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough --skipping training candidate: Tm1_i4.p1, not unique enough +-skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough -skipping training candidate: Tm1_i11.p1, not unique enough --skipping training candidate: Tm1_i3.p1, not unique enough --skipping training candidate: Tm1_i6.p1, not unique enough +-skipping training candidate: Tm1_i4.p1, not unique enough +-skipping training candidate: Npl4_i3.p2, not unique enough -skipping training candidate: Npl4_i2.p2, not unique enough --skipping training candidate: Npl4_i1.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough --skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough --skipping training candidate: CG8312_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: Dgk_i7.p2, not unique enough --skipping training candidate: eIF5B_i3.p2, not unique enough --skipping training candidate: eIF5B_i1.p2, not unique enough -skipping training candidate: eIF5B_i2.p2, not unique enough -skipping training candidate: eIF5B_i4.p2, not unique enough --skipping training candidate: Dgk_i6.p2, not unique enough +-skipping training candidate: eIF5B_i3.p2, not unique enough +-skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough -skipping training candidate: Dgk_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_i1.p3, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough --skipping training candidate: Dgk_i4.p3, not unique enough --skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough -skipping training candidate: Dgk_i3.p3, not unique enough +-skipping training candidate: Dgk_i6.p3, not unique enough +-skipping training candidate: Dgk_i4.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough +-skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: l(3)05822_i3.p3, not unique enough --skipping training candidate: l(3)05822_i4.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_i2.p3, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough --skipping training candidate: CG13887_i2.p1, not unique enough +-skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG14995_i7.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough -skipping training candidate: nmo_i7.p2, not unique enough +-skipping training candidate: nmo_i4.p2, not unique enough +-skipping training candidate: nmo_i6.p2, not unique enough +-skipping training candidate: nmo_i3.p2, not unique enough -skipping training candidate: nmo_i5.p2, not unique enough --skipping training candidate: nmo_i1.p2, not unique enough -skipping training candidate: nmo_i2.p2, not unique enough --skipping training candidate: nmo_i6.p2, not unique enough --skipping training candidate: nmo_i4.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough --skipping training candidate: gukh_i1.p2, not unique enough -skipping training candidate: gukh_i3.p2, not unique enough +-skipping training candidate: gukh_i1.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_i5.p1, not unique enough -skipping training candidate: RpL15_i2.p1, not unique enough --skipping training candidate: RpL15_i4.p1, not unique enough -skipping training candidate: RpL15_i1.p1, not unique enough +-skipping training candidate: RpL15_i4.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_i3.p3, not unique enough -skipping training candidate: Npl4_i2.p3, not unique enough --skipping training candidate: Npl4_i1.p3, not unique enough --skipping training candidate: trc_i2.p2, not unique enough +-skipping training candidate: trc_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i1.p3, not unique enough -skipping training candidate: Hsc70-1_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough --skipping training candidate: CG14995_i4.p2, not unique enough --skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough --skipping training candidate: CG10237_i5.p2, not unique enough --skipping training candidate: CG10237_i3.p2, not unique enough --skipping training candidate: CG10237_i1.p2, not unique enough +-skipping training candidate: CG14995_i1.p2, not unique enough +-skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG10237_i2.p2, not unique enough +-skipping training candidate: CG10237_i3.p2, not unique enough +-skipping training candidate: CG10237_i5.p2, not unique enough +-skipping training candidate: CG10237_i4.p2, not unique enough -skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Eno_i3.p3, not unique enough --skipping training candidate: Eno_i2.p3, not unique enough --skipping training candidate: Eno_i1.p3, not unique enough +-skipping training candidate: Eno_i6.p3, not unique enough -skipping training candidate: Eno_i5.p3, not unique enough --skipping training candidate: Sec16_i1.p3, not unique enough +-skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough +-skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough -skipping training candidate: gukh_i2.p2, not unique enough --skipping training candidate: ATPsyn-d_i1.p1, 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_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough --skipping training candidate: CG30438_i5.p2, not unique enough --skipping training candidate: CG30438_i4.p2, not unique enough --skipping training candidate: CG30438_i3.p2, not unique enough -skipping training candidate: CG30438_i1.p2, not unique enough +-skipping training candidate: CG30438_i2.p2, not unique enough +-skipping training candidate: CG30438_i3.p2, not unique enough +-skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough --skipping training candidate: cdi_i1.p3, not unique enough --skipping training candidate: CG14995_i4.p3, not unique enough --skipping training candidate: CG14995_i1.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_i1.p3, not unique enough +-skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CanB2_i2.p1, not unique enough --skipping training candidate: ADD1_i2.p2, not unique enough --skipping training candidate: Sec16_i1.p4, 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_i3.p3, not unique enough -skipping training candidate: bic_i2.p1, not unique enough --skipping training candidate: CG12581_i1.p2, not unique enough +-skipping training candidate: CG12581_i2.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough --skipping training candidate: ctp_i1.p1, not unique enough -skipping training candidate: ctp_i4.p1, not unique enough --skipping training candidate: ctp_i2.p1, not unique enough +-skipping training candidate: ctp_i1.p1, not unique enough +-skipping training candidate: ctp_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_i3.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: Eno_i6.p4, not unique enough -skipping training candidate: Eno_i5.p4, not unique enough --skipping training candidate: Klp10A_i5.p3, not unique enough --skipping training candidate: Klp10A_i4.p3, not unique enough +-skipping training candidate: Eno_i2.p4, not unique enough +-skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Klp10A_i3.p3, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Klp10A_i6.p3, not unique enough --skipping training candidate: Klp10A_i2.p4, not unique enough +-skipping training candidate: Klp10A_i4.p3, not unique enough -skipping training candidate: Calx_i8.p2, not unique enough --skipping training candidate: Calx_i7.p3, not unique enough --skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough --skipping training candidate: Calx_i1.p2, not unique enough --skipping training candidate: Calx_i2.p2, not unique enough -skipping training candidate: Calx_i6.p2, not unique enough --skipping training candidate: CG7564_i1.p2, not unique enough +-skipping training candidate: 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_i2.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_i3.p3, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough --skipping training candidate: CG7564_i3.p3, not unique enough +-skipping training candidate: CG7564_i1.p2, not unique enough +-skipping training candidate: CG7564_i1.p3, not unique enough -skipping training candidate: Gale_i1.p2, not unique enough --skipping training candidate: eIF5B_i3.p3, not unique enough --skipping training candidate: eIF5B_i1.p3, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough -skipping training candidate: eIF5B_i4.p3, not unique enough +-skipping training candidate: eIF5B_i3.p3, not unique enough +-skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough --skipping training candidate: AdipoR_i4.p2, not unique enough +-skipping training candidate: AdipoR_i3.p2, not unique enough -skipping training candidate: CG6424_i2.p3, not unique enough --skipping training candidate: CG6424_i4.p3, not unique enough -skipping training candidate: CG6424_i1.p3, not unique enough -skipping training candidate: CG6424_i1.p4, not unique enough --skipping training candidate: Tm1_i16.p2, not unique enough +-skipping training candidate: CG6424_i4.p3, not unique enough -skipping training candidate: Tm1_i5.p2, not unique enough +-skipping training candidate: Tm1_i14.p2, not unique enough -skipping training candidate: Tm1_i13.p2, not unique enough --skipping training candidate: Dgk_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: Dgk_i7.p5, not unique enough --skipping training candidate: Dgk_i3.p4, not unique enough --skipping training candidate: cdi_i1.p4, not unique enough +-skipping training candidate: cdi_i2.p3, not unique enough +-skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: eff_i1.p1, not unique enough --skipping training candidate: eff_i2.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough --skipping training candidate: eIF5B_i3.p4, not unique enough --skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough -skipping training candidate: eIF5B_i4.p5, not unique enough --skipping training candidate: Sec16_i3.p4, not unique enough --skipping training candidate: Sec16_i1.p5, not unique enough +-skipping training candidate: eIF5B_i3.p4, not unique enough +-skipping training candidate: eIF5B_i5.p4, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough +-skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough --skipping training candidate: CG32082_i4.p2, not unique enough --skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: Sec16_i3.p4, not unique enough -skipping training candidate: CG32082_i3.p2, not unique enough +-skipping training candidate: CG32082_i1.p2, not unique enough +-skipping training candidate: CG32082_i2.p2, not unique enough +-skipping training candidate: CG3530_i3.p2, not unique enough -skipping training candidate: CG3530_i2.p2, not unique enough --skipping training candidate: CG3530_i1.p2, not unique enough -skipping training candidate: Dgk_i7.p6, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough +-skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: l(3)05822_i3.p4, not unique enough --skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: sqd_i2.p2, not unique enough --skipping training candidate: CG7564_i2.p6, not unique enough --skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: CG7564_i3.p4, not unique enough +-skipping training candidate: CG7564_i4.p4, not unique enough +-skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: S-Lap3_i2.p2, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough --skipping training candidate: cdi_i1.p5, 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_i1.p2, not unique enough -skipping training candidate: CG6091_i2.p2, not unique enough -skipping training candidate: CG6091_i3.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_i4.p2, not unique enough -skipping training candidate: Cnx99A_i2.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: Sec16_i3.p5, not unique enough --skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i6.p4, not unique enough --skipping training candidate: ogre_i6.p2, not unique enough +-skipping training candidate: Sec16_i1.p6, not unique enough +-skipping training candidate: Sec16_i3.p5, not unique enough +-skipping training candidate: ogre_i3.p2, not unique enough -skipping training candidate: CG6024_i2.p3, not unique enough -skipping training candidate: hrg_i1.p3, not unique enough -skipping training candidate: hrg_i4.p3, not unique enough --skipping training candidate: ATPsyn-d_i3.p2, not unique enough --skipping training candidate: CG6091_i4.p3, not unique enough +-skipping training candidate: ATPsyn-d_i1.p2, not unique enough +-skipping training candidate: CG6091_i1.p3, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough -skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: CG33970_i3.p2, not unique enough --skipping training candidate: eIF5B_i5.p5, not unique enough --skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough +-skipping training candidate: eIF5B_i3.p5, not unique enough +-skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: Aldh-III_i8.p2, not unique enough --skipping training candidate: Aldh-III_i10.p2, not unique enough --skipping training candidate: CG13284_i5.p2, not unique enough +-skipping training candidate: Aldh-III_i11.p2, not unique enough -skipping training candidate: CG13284_i3.p2, not unique enough -skipping training candidate: CG13284_i1.p2, not unique enough -skipping training candidate: CG13284_i2.p2, not unique enough --skipping training candidate: Lip4_i1.p2, not unique enough +-skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: Lip4_i3.p2, not unique enough +-skipping training candidate: Lip4_i2.p2, not unique enough +-skipping training candidate: Dgk_i3.p5, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough --skipping training candidate: Dgk_i2.p7, not unique enough --skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough +-skipping training candidate: Dgk_i4.p4, not unique enough +-skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Dgk_i7.p7, not unique enough --skipping training candidate: Dgk_i3.p5, not unique enough --skipping training candidate: Tm1_i16.p3, not unique enough -skipping training candidate: Tm1_i5.p3, not unique enough +-skipping training candidate: Tm1_i14.p3, not unique enough -skipping training candidate: Tm1_i13.p3, not unique enough +-skipping training candidate: CG8312_i1.p2, not unique enough +-skipping training candidate: CG8312_i1.p3, not unique enough -skipping training candidate: CG8312_i2.p3, not unique enough -skipping training candidate: CG8312_i2.p4, not unique enough --skipping training candidate: CG8312_i4.p3, not unique enough --skipping training candidate: CG8312_i4.p4, not unique enough -skipping training candidate: CG8312_i3.p3, not unique enough -skipping training candidate: CG8312_i3.p4, not unique enough --skipping training candidate: Klp10A_i5.p4, not unique enough --skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i3.p4, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough -skipping training candidate: Klp10A_i6.p4, not unique enough --skipping training candidate: Klp10A_i2.p6, not unique enough +-skipping training candidate: Klp10A_i4.p4, not unique enough +-skipping training candidate: eff_i3.p2, not unique enough -skipping training candidate: eff_i1.p2, not unique enough --skipping training candidate: eff_i2.p2, not unique enough --skipping training candidate: CG14995_i4.p4, not unique enough --skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough +-skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i7.p4, not unique enough -skipping training candidate: CG14995_i6.p4, not unique enough +-skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG6424_i2.p4, not unique enough --skipping training candidate: CG6424_i4.p4, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough --skipping training candidate: CG12581_i1.p3, not unique enough --skipping training candidate: CG32082_i4.p5, not unique enough --skipping training candidate: CG32082_i1.p3, not unique enough +-skipping training candidate: CG6424_i4.p4, not unique enough +-skipping training candidate: CG12581_i2.p3, not unique enough -skipping training candidate: CG32082_i3.p3, not unique enough +-skipping training candidate: CG32082_i1.p3, not unique enough +-skipping training candidate: CG32082_i2.p3, not unique enough +-skipping training candidate: Cnx99A_i2.p3, not unique enough -skipping training candidate: Cnx99A_i3.p3, not unique enough --skipping training candidate: Cnx99A_i1.p3, not unique enough +-skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Cdep_i2.p6, not unique enough --skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough -skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: CG33970_i3.p3, not unique enough --skipping training candidate: Sec16_i3.p6, not unique enough --skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: Sec16_i6.p5, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough +-skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough +-skipping training candidate: Sec16_i3.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough -skipping training candidate: CG6024_i2.p4, not unique enough --skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Myo61F_i4.p2, not unique enough +-skipping training candidate: Myo61F_i3.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_i2.p4, not unique enough -skipping training candidate: Cnx99A_i3.p4, not unique enough --skipping training candidate: Cnx99A_i1.p4, not unique enough -skipping training candidate: CG13887_i1.p2, not unique enough --skipping training candidate: CG13887_i2.p2, not unique enough +-skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough --skipping training candidate: CG6145_i4.p2, not unique enough --skipping training candidate: CG6145_i3.p2, not unique enough +-skipping training candidate: CG6145_i2.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_i8.p3, not unique enough --skipping training candidate: Calx_i7.p5, not unique enough --skipping training candidate: Calx_i9.p3, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough -skipping training candidate: Calx_i4.p3, 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_i6.p3, not unique enough --skipping training candidate: mge_i1.p2, 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_i2.p3, not unique enough +-skipping training candidate: mge_i2.p2, not unique enough +-skipping training candidate: AdipoR_i4.p3, not unique enough +-skipping training candidate: AdipoR_i3.p3, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough -skipping training candidate: AdipoR_i5.p2, not unique enough --skipping training candidate: AdipoR_i4.p3, not unique enough --skipping training candidate: AdipoR_i1.p2, not unique enough --skipping training candidate: Aldh-III_i4.p2, not unique enough --skipping training candidate: Aldh-III_i6.p2, not unique enough --skipping training candidate: Aldh-III_i1.p2, not unique enough --skipping training candidate: Aldh-III_i10.p3, not unique enough +-skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Aldh-III_i7.p2, not unique enough +-skipping training candidate: Aldh-III_i1.p2, not unique enough +-skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough --skipping training candidate: Cdep_i1.p4, not unique enough --skipping training candidate: Cdep_i2.p9, not unique enough +-skipping training candidate: Aldh-III_i4.p2, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough +-skipping training candidate: Cdep_i4.p3, not unique enough +-skipping training candidate: Cdep_i2.p9, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: hrg_i2.p2, not unique enough -skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough --skipping training candidate: CG12581_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_i1.p8, not unique enough --skipping training candidate: Sec16_i1.p9, not unique enough +-skipping training candidate: CG12581_i2.p4, 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_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: 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: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough --skipping training candidate: CG6091_i4.p4, not unique enough +-skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i2.p3, not unique enough -skipping training candidate: CG6091_i3.p4, not unique enough -skipping training candidate: CanB2_i2.p2, not unique enough -skipping training candidate: IP3K1_i2.p2, not unique enough --skipping training candidate: Klp10A_i5.p5, not unique enough --skipping training candidate: Klp10A_i4.p5, not unique enough +-skipping training candidate: Klp10A_i2.p8, not unique enough +-skipping training candidate: Klp10A_i3.p5, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: Klp10A_i6.p5, not unique enough --skipping training candidate: Klp10A_i2.p8, not unique enough +-skipping training candidate: Klp10A_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_i2.p10, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough --skipping training candidate: Est-6_i1.p2, not unique enough --skipping training candidate: Klp10A_i5.p6, not unique enough --skipping training candidate: Klp10A_i4.p6, not unique enough +-skipping training candidate: Cdep_i4.p4, not unique enough +-skipping training candidate: Cdep_i2.p10, not unique enough +-skipping training candidate: Est-6_i2.p2, not unique enough +-skipping training candidate: Klp10A_i2.p9, 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_i6.p6, not unique enough --skipping training candidate: Klp10A_i2.p9, not unique enough +-skipping training candidate: Klp10A_i4.p6, not unique enough -skipping training candidate: 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_i4.p3, not unique enough -skipping training candidate: Cnx99A_i2.p5, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough --skipping training candidate: Cnx99A_i1.p5, not unique enough --skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i4.p3, not unique enough +-skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough --skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: Myo61F_i4.p4, not unique enough +-skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough -skipping training candidate: bic_i2.p2, not unique enough -skipping training candidate: CG10082_i2.p3, not unique enough --skipping training candidate: CG32082_i4.p6, not unique enough --skipping training candidate: CG32082_i1.p4, not unique enough -skipping training candidate: CG32082_i3.p4, not unique enough +-skipping training candidate: CG32082_i1.p4, not unique enough +-skipping training candidate: CG32082_i2.p4, not unique enough -skipping training candidate: Eno_i4.p6, not unique enough -skipping training candidate: Eno_i3.p5, not unique enough --skipping training candidate: Eno_i2.p5, not unique enough --skipping training candidate: Eno_i1.p6, not unique enough +-skipping training candidate: Eno_i6.p5, not unique enough -skipping training candidate: Eno_i5.p6, not unique enough --skipping training candidate: Sec16_i3.p9, not unique enough +-skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i4.p10, not unique enough +-skipping training candidate: Sec16_i3.p9, 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_i2.p8, not unique enough --skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i5.p5, not unique enough +-skipping training candidate: Dgk_i4.p5, not unique enough +-skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i7.p8, not unique enough --skipping training candidate: Dgk_i3.p6, not unique enough --skipping training candidate: nmo_i4.p3, not unique enough +-skipping training candidate: nmo_i6.p3, not unique enough -skipping training candidate: CG33970_i1.p4, not unique enough --skipping training candidate: sqd_i3.p2, 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: Dgk_i3.p7, not unique enough +-skipping training candidate: His4r_i3.p1, not unique enough -skipping training candidate: His4r_i2.p1, not unique enough -skipping training candidate: 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: Hsc70-1_i3.p4, not unique enough -skipping training candidate: hrg_i1.p5, not unique enough -skipping training candidate: hrg_i4.p6, not unique enough --skipping training candidate: CG8136_i3.p2, not unique enough --skipping training candidate: CG8136_i4.p2, not unique enough +-skipping training candidate: CG8136_i1.p2, not unique enough -skipping training candidate: CG8136_i2.p2, not unique enough --skipping training candidate: Myo61F_i3.p5, not unique enough +-skipping training candidate: CG8136_i3.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_i2.p5, not unique enough --skipping training candidate: CG6091_i4.p5, not unique enough +-skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i2.p4, not unique enough -skipping training candidate: CG6091_i3.p5, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough --skipping training candidate: CG6145_i4.p3, not unique enough --skipping training candidate: CG6145_i3.p3, not unique enough +-skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i1.p3, not unique enough +-skipping training candidate: CG6145_i4.p3, not unique enough -skipping training candidate: gukh_i2.p3, not unique enough --skipping training candidate: sqd_i3.p3, not unique enough +-skipping training candidate: sqd_i5.p4, not unique enough -skipping training candidate: CG33125_i1.p4, not unique enough -skipping training candidate: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% -* [Fri Apr 10 07:35:05 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 +* [Sun Mar 9 03:28:21 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 PCT_GC: 49.4 -* [Fri Apr 10 07:35:05 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 -* [Fri Apr 10 07:35:06 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 -* [Fri Apr 10 07:35:12 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 +* [Sun Mar 9 03:28:21 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 +* [Sun Mar 9 03:28:23 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 +* [Sun Mar 9 03:28:34 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 Selecting best orfs -* [Fri Apr 10 07:35:12 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* [Fri Apr 10 07:35:12 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 -* [Fri Apr 10 07:35:13 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 +* [Sun Mar 9 03:28:35 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* [Sun Mar 9 03:28:35 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 +* [Sun Mar 9 03:28:36 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:35:46 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 +* [Sun Mar 9 03:29:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores -* [Fri Apr 10 07:35:54 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 || : +* [Sun Mar 9 03:29:52 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 -* [Fri Apr 10 07:35:55 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 +* [Sun Mar 9 03:29:54 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 null device 1 -* [Fri Apr 10 07:35:56 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 || : +* [Sun Mar 9 03:29:56 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:35:56 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 || : +* [Sun Mar 9 03:29:57 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 -* [Fri Apr 10 07:35:57 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 +* [Sun Mar 9 03:29:58 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/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: -1.3119246248475 instead of -3.41867986556031 --feature swap of score: -1.20233901434502 instead of -3.32711795084951 --feature swap of score: -1.98643392083423 instead of -3.0347360268129 --feature swap of score: -1.31808638404514 instead of -1.86132376280058 --feature swap of score: -0.958792391852879 instead of -1.33016837557081 --feature swap of score: -0.579291859747031 instead of -0.988731056140854 --feature swap of score: 1.89124211322284 instead of -2.17929842461196 --feature swap of score: -1.03502182740319 instead of -1.55020972219232 --feature swap of score: 2.48410923576907 instead of -1.43320122282501 --feature swap of score: 1.2948358274397 instead of -1.21068111782346 --feature swap of score: -0.552464033332304 instead of -1.16903564374517 --feature swap of score: -0.00701951658508154 instead of -1.03561172117999 --feature swap of score: 0.719286041112863 instead of -1.20029074299099 --feature swap of score: 1.98821003203635 instead of -1.14866006018312 --feature swap of score: 0.723443604466109 instead of -0.922899515358874 --feature swap of score: -0.336483919589463 instead of -1.07795861636303 --feature swap of score: 1.16775083415801 instead of -0.969190605417256 --feature swap of score: -0.0891918199072498 instead of -0.822368981168256 --feature swap of score: -0.674511128985883 instead of -0.978185504796567 --feature swap of score: 0.420293920576897 instead of -0.603583519437177 --feature swap of score: 3.22754009977781 instead of -0.339909650016304 --feature swap of score: 1.50647891651405 instead of -0.200908740096265 --feature swap of score: 2.73997165094754 instead of -0.198608247604753 --feature swap of score: -0.0649572533848136 instead of -0.163683372192632 --feature swap of score: 1.73819181460049 instead of -0.242817388363713 --feature swap of score: 1.73094093593958 instead of -0.04278867302864 --feature swap of score: -0.204795425807676 instead of -0.516905906069618 --feature swap of score: 1.34137377970011 instead of -0.595718492060707 --feature swap of score: 0.0315879135088422 instead of -0.107155148209247 --feature swap of score: 0.755013244542518 instead of -0.106177835272599 --feature swap of score: 0.529746622883219 instead of 0.174846823485462 --feature swap of score: 1.31109820543825 instead of 0.126092029779623 --feature swap of score: 1.64884176250758 instead of -0.179400612309685 --feature swap of score: 1.04031808204722 instead of -0.0454687102881514 --feature swap of score: 1.78956473326178 instead of -0.234704007107249 --feature swap of score: 3.02596255144534 instead of -0.435152230293133 --feature swap of score: -0.218037445236893 instead of -0.307625386994569 --feature swap of score: 1.86074135616739 instead of -0.424768451970943 --feature swap of score: 0.406864466507634 instead of -0.126667499643164 --feature swap of score: 0.19355854688519 instead of -0.0896685849058075 --feature swap of score: 3.35963985661364 instead of 0.14056054929966 --feature swap of score: 1.57608901965423 instead of 0.224292313728416 --feature swap of score: 1.32403267720349 instead of 0.219259164942379 --feature swap of score: 0.451066466920039 instead of 0.0462509915563394 --feature swap of score: 2.32584195429512 instead of 0.142183081788314 --feature swap of score: 1.26478083091475 instead of 0.308295880862111 --feature swap of score: 2.10115855532356 instead of 0.466066204515709 --feature swap of score: 2.19149184357001 instead of 0.46907473188828 --feature swap of score: 1.71692071056652 instead of 0.440414430738255 --feature swap of score: 3.10264011194856 instead of 0.469020969578799 --feature swap of score: 3.49574081425016 instead of -0.285266802955967 --feature swap of score: 1.4228167576644 instead of 0.20013521424683 --feature swap of score: 0.974132742788869 instead of 0.166233833936864 --feature swap of score: 5.12260826228945 instead of 0.526011856698564 --feature swap of score: 2.58873836544667 instead of 0.46782863588236 --num feature swaps: 55 -* [Fri Apr 10 07:35:57 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 +-feature swap of score: -1.36352199191982 instead of -3.58934776599398 +-feature swap of score: -1.45462975921351 instead of -3.45774649367825 +-feature swap of score: -1.81444377220324 instead of -3.00217340841227 +-feature swap of score: -1.09477432788552 instead of -1.51051889890666 +-feature swap of score: -0.896658712117579 instead of -1.28721339508026 +-feature swap of score: 1.79238089060951 instead of -1.22110863411787 +-feature swap of score: -0.552371082247238 instead of -0.98293595289854 +-feature swap of score: 2.91326363960109 instead of -1.08520097309725 +-feature swap of score: -0.737860205076349 instead of -0.837010271589923 +-feature swap of score: -1.47431834009232 instead of -2.08511301750635 +-feature swap of score: 2.18770374052349 instead of -1.35877837594694 +-feature swap of score: -0.992442171446657 instead of -1.42683185130935 +-feature swap of score: 0.528147606043592 instead of -1.43487848718437 +-feature swap of score: 1.22198874425744 instead of -1.30262748850186 +-feature swap of score: 1.89617911563358 instead of -1.2872622114438 +-feature swap of score: 0.316902056856975 instead of -1.14803527612745 +-feature swap of score: -0.1072372339357 instead of -1.1752549922722 +-feature swap of score: -0.152140745712907 instead of -1.25491028008822 +-feature swap of score: -0.336671259497742 instead of -1.01143958157026 +-feature swap of score: -0.828672832898478 instead of -0.846215298065208 +-feature swap of score: 0.514435449134003 instead of -0.511997886888063 +-feature swap of score: 2.98420498104939 instead of -0.433954102630498 +-feature swap of score: 1.83353263133999 instead of -0.534588138492826 +-feature swap of score: 0.0307091490736576 instead of -0.47139837263928 +-feature swap of score: 2.44106688688763 instead of -0.573006873261511 +-feature swap of score: 0.739214012769349 instead of -0.57459375881032 +-feature swap of score: 2.21036250698655 instead of -0.803552147972103 +-feature swap of score: 1.21996956671894 instead of -0.914716814756302 +-feature swap of score: 1.21049596763716 instead of -0.6007099440788 +-feature swap of score: 0.935117340427718 instead of -0.424821941475044 +-feature swap of score: 3.64162097057363 instead of -0.717040853618008 +-feature swap of score: 1.59146575629038 instead of -0.728644165358737 +-feature swap of score: 0.857636019872111 instead of -1.05113743805405 +-feature swap of score: -0.910474894324282 instead of -1.21550389827886 +-feature swap of score: 1.02558295772055 instead of -1.30199746205694 +-feature swap of score: 1.13498835669287 instead of -0.993486554603171 +-feature swap of score: 0.604415495192346 instead of -0.456732682653071 +-feature swap of score: -0.200343990900423 instead of -0.517127592917244 +-feature swap of score: 0.556326951755164 instead of -0.408799467682449 +-feature swap of score: 0.0952023284412004 instead of -0.411828177712754 +-feature swap of score: 2.45339254962817 instead of -0.396263646169375 +-feature swap of score: 0.776699712696392 instead of -0.294499977943052 +-feature swap of score: 1.63528459789488 instead of -0.089657523532745 +-feature swap of score: 0.947924289225011 instead of 0.227821688824539 +-feature swap of score: 1.07122589369871 instead of 0.233083200003931 +-feature swap of score: 0.184641894912175 instead of -0.125247287386679 +-feature swap of score: 1.30047393210982 instead of -0.176046296311308 +-feature swap of score: 1.14079814319604 instead of -0.0864093043119786 +-feature swap of score: 0.630527452629068 instead of -0.036393979942617 +-feature swap of score: 2.5338991444975 instead of 0.0542684271949185 +-feature swap of score: 1.01638455115272 instead of 0.189408018089965 +-feature swap of score: 0.786453729522419 instead of 0.00831628213611529 +-feature swap of score: 2.45347497287016 instead of 0.128916820780523 +-feature swap of score: 1.05582292300041 instead of 0.23371676999617 +-feature swap of score: 0.285699981933035 instead of 0.144726063173848 +-feature swap of score: 0.562402766888401 instead of 0.0463842756575228 +-feature swap of score: 8.38177432334784 instead of -0.105665990649193 +-feature swap of score: 1.8481647361741 instead of 0.460842450536775 +-feature swap of score: 3.11248821716954 instead of 0.559353655626095 +-feature swap of score: 9.58781280226133 instead of 0.528990548987455 +-num feature swaps: 60 +* [Sun Mar 9 03:29:59 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 -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 -* [Fri Apr 10 07:36:29 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/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 +* [Sun Mar 9 03:31:16 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/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores -* [Fri Apr 10 07:36:37 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : +* [Sun Mar 9 03:31:32 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 || : null device 1 -* [Fri Apr 10 07:36:38 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc +* [Sun Mar 9 03:31:34 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 -* [Fri Apr 10 07:36:39 2026] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : +* [Sun Mar 9 03:31:37 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 || : Loading required package: grid null device 1 -* [Fri Apr 10 07:36:40 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 +* [Sun Mar 9 03:31:38 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 Refining start codon selections. --number of revised start positions: 11 -* [Fri Apr 10 07:36:40 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* [Fri Apr 10 07:36:40 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/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed +-number of revised start positions: 13 +* [Sun Mar 9 03:31:38 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* [Sun Mar 9 03:31:38 2025] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed -* [Fri Apr 10 07:36:40 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/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 +* [Sun Mar 9 03:31:39 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 Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep -* [Fri Apr 10 07:36:40 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/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 +* [Sun Mar 9 03:31:39 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 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.* @@ -13675,8 +13716,8 @@ -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. --Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. --Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. +-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.p7. -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. -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. @@ -13818,12 +13859,14 @@ 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/34036/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/34036/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/123159 and its subdirectories -I: Current time: Fri Apr 10 07:36:57 -12 2026 -I: pbuilder-time-stamp: 1775849817 +I: removing directory /srv/workspace/pbuilder/34036 and its subdirectories +I: Current time: Sun Mar 9 03:32:13 +14 2025 +I: pbuilder-time-stamp: 1741440733