# HG changeset patch # User iuc # Date 1576868933 18000 # Node ID ca6d970d931c8be13eea0d136a0795ca280c9f93 # Parent b3f5d0879dab880a36e417aac7b41a445fe7cdc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1" diff -r b3f5d0879dab -r ca6d970d931c augustus.xml --- a/augustus.xml Thu May 23 18:17:05 2019 -0400 +++ b/augustus.xml Fri Dec 20 14:08:53 2019 -0500 @@ -10,7 +10,7 @@ ## Using an augustus model from history, we need to unzip it and let augustus find it - cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && + cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ && mkdir -p 'augustus_dir/species/' && diff -r b3f5d0879dab -r ca6d970d931c macros.xml --- a/macros.xml Thu May 23 18:17:05 2019 -0400 +++ b/macros.xml Fri Dec 20 14:08:53 2019 -0500 @@ -7,7 +7,7 @@ - 3.2.3 + 3.3.3 diff -r b3f5d0879dab -r ca6d970d931c test-data/augustus.hints.output.gtf --- a/test-data/augustus.hints.output.gtf Thu May 23 18:17:05 2019 -0400 +++ b/test-data/augustus.hints.output.gtf Fri Dec 20 14:08:53 2019 -0500 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat ... +# reading in the file /tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # fly version. Using default transition matrix. -# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9950, name = chr2R) ----- @@ -40,144 +40,10 @@ # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features # Deleted 23 groups because some hint was not satisfiable. -# Constraints/Hints: -chr2R w2h ep 7551 7560 5.3 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 7561 7570 7.4 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 7571 7580 9.7 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7581 7590 10.2 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 7591 7600 9 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7601 7610 9.7 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7611 7620 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7621 7630 15.3 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 7631 7640 13.4 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7641 7650 13.7 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7651 7660 14.4 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7661 7670 14.6 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7671 7680 16.8 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7681 7690 16.7 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7691 7700 17.6 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7701 7710 20.3 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7711 7720 20.5 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7721 7730 18.8 . . mult=18;src=W "1.17304;0.992;35:0" -chr2R w2h ep 7731 7740 16.7 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7741 7750 16.8 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7751 7760 15.5 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 7761 7770 17.4 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7771 7780 19.5 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7781 7790 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7791 7800 20.1 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7801 7810 22.7 . . mult=22;src=W "1.21988;0.992;43:0" -chr2R w2h ep 7811 7820 24.4 . . mult=24;src=W "1.24409;0.992;47:0" -chr2R w2h ep 7821 7830 23.6 . . mult=23;src=W "1.23192;0.992;45:0" -chr2R w2h ep 7831 7840 19.5 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7841 7850 16.2 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7851 7860 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7861 7870 14 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7871 7880 14.3 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7881 7890 11.4 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 7891 7900 12.9 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 7901 7910 14 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7911 7920 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7921 7930 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7931 7940 14.2 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7941 7950 11.8 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 7951 7960 13.3 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7961 7970 13.7 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7971 7980 12.4 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 7981 7990 17.1 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7991 8000 19.9 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8001 8010 20 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 8011 8020 22.7 . . mult=22;src=W "1.21988;0.992;43:0" -chr2R w2h ep 8021 8030 21.9 . . mult=21;src=W "1.20797;0.992;41:0" -chr2R w2h ep 8031 8040 21 . . mult=21;src=W "1.20797;0.992;41:0" -chr2R w2h ep 8041 8050 25.1 . . mult=25;src=W "1.25639;0.992;49:0" -chr2R w2h ep 8051 8060 23.5 . . mult=23;src=W "1.23192;0.992;45:0" -chr2R w2h ep 8061 8070 20.3 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 8071 8080 19.8 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8081 8090 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8091 8100 15.4 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8101 8110 15.8 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8111 8120 12.5 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 8121 8130 9.4 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8131 8140 5.8 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8210 8219 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8220 8229 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8230 8239 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8240 8249 5 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8260 8269 4.8 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8270 8279 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8280 8289 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8290 8299 7.3 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8300 8309 7 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8310 8319 7.3 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8320 8329 9.6 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8330 8339 11.6 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8340 8349 10.8 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8350 8359 10.1 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8360 8369 11 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8370 8379 13.4 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8380 8389 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8390 8399 11.8 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8400 8409 9 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8410 8419 7.7 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8420 8429 8.9 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8430 8439 11.5 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8440 8449 11.4 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8450 8459 9.8 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8460 8469 10.2 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8470 8479 10.8 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8480 8489 10 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8490 8499 8.2 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8500 8509 7.1 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8510 8519 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8520 8529 4.7 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8739 8748 4.3 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8749 8758 5.7 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8759 8768 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8769 8778 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8779 8788 8.6 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8789 8798 8.7 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8880 8889 12.7 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 8890 8899 15.3 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8900 8909 17.6 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8910 8919 17.9 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8920 8929 17.2 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8930 8939 18.4 . . mult=18;src=W "1.17304;0.992;35:0" -chr2R w2h ep 8940 8949 19.9 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8950 8959 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8960 8969 15.2 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8970 8979 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8980 8989 14.7 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 8990 8999 14.5 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 9000 9009 14.5 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 9010 9019 12.5 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9020 9029 11.9 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 9030 9039 12.1 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9040 9049 10 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 9050 9059 9.7 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 9060 9069 10.6 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 9070 9079 12.3 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9080 9089 13.1 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 9090 9099 13.4 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 9100 9109 12 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9110 9119 10.7 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 9120 9129 11 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 9130 9139 10.9 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 9140 9149 7.9 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 9150 9159 4.9 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 9160 9169 4.4 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 9265 9274 11.4 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 9275 9284 12.8 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9285 9294 13.1 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 9295 9304 13.6 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 9305 9314 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 9315 9324 12.4 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 9325 9334 9 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 9335 9344 5.2 . . mult=5;src=W "1.03743;0.992;9:0" # Predicted genes for sequence number 1 on both strands # start gene chr2R.g1 -chr2R AUGUSTUS gene 7560 9303 0.79 - . chr2R.g1 -chr2R AUGUSTUS transcript 7560 9303 0.79 - . chr2R.g1.t1 +chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1 +chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1 chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 57.1 @@ -192,4 +58,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_15.dat --species=fly \ No newline at end of file +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/8/9/2/dataset_8920e51c-dd38-4e36-abf4-14825237cd41.dat --species=fly diff -r b3f5d0879dab -r ca6d970d931c test-data/augustus.hints_and_range.output.gtf --- a/test-data/augustus.hints_and_range.output.gtf Thu May 23 18:17:05 2019 -0400 +++ b/test-data/augustus.hints_and_range.output.gtf Fri Dec 20 14:08:53 2019 -0500 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat ... +# reading in the file /tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # fly version. Using default transition matrix. -# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 2001, name = chr2R) ----- @@ -34,120 +34,10 @@ # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features # Deleted 17 groups because some hint was not satisfiable. -# Constraints/Hints: -chr2R w2h ep 7551 7560 5.3 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 7561 7570 7.4 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 7571 7580 9.7 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7581 7590 10.2 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 7591 7600 9 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7601 7610 9.7 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 7611 7620 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7621 7630 15.3 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 7631 7640 13.4 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7641 7650 13.7 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7651 7660 14.4 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7661 7670 14.6 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7671 7680 16.8 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7681 7690 16.7 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7691 7700 17.6 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7701 7710 20.3 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7711 7720 20.5 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7721 7730 18.8 . . mult=18;src=W "1.17304;0.992;35:0" -chr2R w2h ep 7731 7740 16.7 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7741 7750 16.8 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7751 7760 15.5 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 7761 7770 17.4 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7771 7780 19.5 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7781 7790 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7791 7800 20.1 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 7801 7810 22.7 . . mult=22;src=W "1.21988;0.992;43:0" -chr2R w2h ep 7811 7820 24.4 . . mult=24;src=W "1.24409;0.992;47:0" -chr2R w2h ep 7821 7830 23.6 . . mult=23;src=W "1.23192;0.992;45:0" -chr2R w2h ep 7831 7840 19.5 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 7841 7850 16.2 . . mult=16;src=W "1.15043;0.992;31:0" -chr2R w2h ep 7851 7860 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7861 7870 14 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7871 7880 14.3 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7881 7890 11.4 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 7891 7900 12.9 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 7901 7910 14 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7911 7920 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7921 7930 14.8 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7931 7940 14.2 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 7941 7950 11.8 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 7951 7960 13.3 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7961 7970 13.7 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 7971 7980 12.4 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 7981 7990 17.1 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 7991 8000 19.9 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8001 8010 20 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 8011 8020 22.7 . . mult=22;src=W "1.21988;0.992;43:0" -chr2R w2h ep 8021 8030 21.9 . . mult=21;src=W "1.20797;0.992;41:0" -chr2R w2h ep 8031 8040 21 . . mult=21;src=W "1.20797;0.992;41:0" -chr2R w2h ep 8041 8050 25.1 . . mult=25;src=W "1.25639;0.992;49:0" -chr2R w2h ep 8051 8060 23.5 . . mult=23;src=W "1.23192;0.992;45:0" -chr2R w2h ep 8061 8070 20.3 . . mult=20;src=W "1.19619;0.992;39:0" -chr2R w2h ep 8071 8080 19.8 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8081 8090 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8091 8100 15.4 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8101 8110 15.8 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8111 8120 12.5 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 8121 8130 9.4 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8131 8140 5.8 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8210 8219 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8220 8229 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8230 8239 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8240 8249 5 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8260 8269 4.8 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8270 8279 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8280 8289 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8290 8299 7.3 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8300 8309 7 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8310 8319 7.3 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8320 8329 9.6 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8330 8339 11.6 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8340 8349 10.8 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8350 8359 10.1 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8360 8369 11 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8370 8379 13.4 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8380 8389 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8390 8399 11.8 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8400 8409 9 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8410 8419 7.7 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8420 8429 8.9 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8430 8439 11.5 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8440 8449 11.4 . . mult=11;src=W "1.0964;0.992;21:0" -chr2R w2h ep 8450 8459 9.8 . . mult=9;src=W "1.07589;0.992;17:0" -chr2R w2h ep 8460 8469 10.2 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8470 8479 10.8 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8480 8489 10 . . mult=10;src=W "1.08606;0.992;19:0" -chr2R w2h ep 8490 8499 8.2 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8500 8509 7.1 . . mult=7;src=W "1.05617;0.992;13:0" -chr2R w2h ep 8510 8519 4.2 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8520 8529 4.7 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8739 8748 4.3 . . mult=4;src=W "1.02857;0.992;7:0" -chr2R w2h ep 8749 8758 5.7 . . mult=5;src=W "1.03743;0.992;9:0" -chr2R w2h ep 8759 8768 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8769 8778 8 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8779 8788 8.6 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8789 8798 8.7 . . mult=8;src=W "1.06592;0.992;15:0" -chr2R w2h ep 8880 8889 12.7 . . mult=12;src=W "1.1069;0.992;23:0" -chr2R w2h ep 8890 8899 15.3 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8900 8909 17.6 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8910 8919 17.9 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8920 8929 17.2 . . mult=17;src=W "1.16167;0.992;33:0" -chr2R w2h ep 8930 8939 18.4 . . mult=18;src=W "1.17304;0.992;35:0" -chr2R w2h ep 8940 8949 19.9 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8950 8959 19.1 . . mult=19;src=W "1.18455;0.992;37:0" -chr2R w2h ep 8960 8969 15.2 . . mult=15;src=W "1.13933;0.992;29:0" -chr2R w2h ep 8970 8979 13 . . mult=13;src=W "1.11756;0.992;25:0" -chr2R w2h ep 8980 8989 14.7 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 8990 8999 14.5 . . mult=14;src=W "1.12838;0.992;27:0" -chr2R w2h ep 9000 9009 14.5 . . mult=14;src=W "1.12838;0.992;27:0" # Predicted genes for sequence number 1 on both strands # start gene chr2R.g1 -chr2R AUGUSTUS gene 7560 8931 0.83 - . chr2R.g1 -chr2R AUGUSTUS transcript 7560 8931 0.83 - . chr2R.g1.t1 +chr2R AUGUSTUS gene 7560 8931 0.84 - . chr2R.g1 +chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1 chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 60 @@ -162,4 +52,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_19.dat --predictionStart=7000 --predictionEnd=9000 --species=fly \ No newline at end of file +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/1/1/0/dataset_1106f730-ecae-4b8f-917b-47cb5fc7334d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly diff -r b3f5d0879dab -r ca6d970d931c test-data/human_augustus_protein_codingseq_introns_cds_main.gtf --- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu May 23 18:17:05 2019 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri Dec 20 14:08:53 2019 -0500 @@ -1,19 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 1 on both strands # start gene HS04636.g1 HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1 @@ -70,8 +68,6 @@ # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 2 on both strands # start gene HS08198.g2 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2 @@ -102,4 +98,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat --UTR=off --genemodel=complete --species=human diff -r b3f5d0879dab -r ca6d970d931c test-data/human_augustus_utr-on.gff --- a/test-data/human_augustus_utr-on.gff Thu May 23 18:17:05 2019 -0400 +++ b/test-data/human_augustus_utr-on.gff Fri Dec 20 14:08:53 2019 -0500 @@ -1,14 +1,14 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/c/2/9/dataset_c29ecb21-0612-4152-8d35-994815171865.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- @@ -103,4 +103,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human +# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/c/2/9/dataset_c29ecb21-0612-4152-8d35-994815171865.dat --UTR=on --genemodel=complete --species=human diff -r b3f5d0879dab -r ca6d970d931c test-data/human_augustus_utr-on.gtf --- a/test-data/human_augustus_utr-on.gtf Thu May 23 18:17:05 2019 -0400 +++ b/test-data/human_augustus_utr-on.gtf Fri Dec 20 14:08:53 2019 -0500 @@ -1,19 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 1 on both strands # start gene HS04636.g1 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1 @@ -72,8 +70,6 @@ # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 2 on both strands # start gene HS08198.g2 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2 @@ -106,4 +102,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat --UTR=on --genemodel=complete --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat --UTR=on --genemodel=complete --species=human