| Previous changeset 5:b3f5d0879dab (2019-05-23) Next changeset 7:09855551d713 (2021-07-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1" |
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modified:
augustus.xml macros.xml test-data/augustus.hints.output.gtf test-data/augustus.hints_and_range.output.gtf test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf |
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| 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 |
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| @@ -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/' && |
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| 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 |
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| @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@VERSION@">3.2.3</token> + <token name="@VERSION@">3.3.3</token> <xml name="citations"> <citations> |
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| 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 |
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| b'@@ -1,17 +1,17 @@\n-# This output was generated with AUGUSTUS (version 3.2.3).\n+# This output was generated with AUGUSTUS (version 3.3.3).\n # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),\n-# O. Keller, S. K\xc3\xb6nig, L. Gerischer and L. Romoth.\n+# O. Keller, S. K\xc3\xb6nig, L. Gerischer, L. Romoth and Katharina Hoff.\n # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n # Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n # Sources of extrinsic information: M RM E W \n # Setting CDSpart local malus: 0.985\n # Setting UTRpart local malus: 0.973\n-# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat ...\n+# reading in the file /tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat ...\n # Have extrinsic information about 1 sequences (in the specified range). \n-# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ...\n+# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...\n # fly version. Using default transition matrix.\n-# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat is in fasta format.\n+# Looks like /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat is in fasta format.\n # We have hints for 1 sequence and for 1 of the sequences in the input set.\n #\n # ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----\n@@ -40,144 +40,10 @@\n # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features\n # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features\n # Deleted 23 groups because some hint was not satisfiable.\n-# Constraints/Hints:\n-chr2R\tw2h\tep\t7551\t7560\t5.3\t.\t.\tmult=5;src=W "1.03743;0.992;9:0"\n-chr2R\tw2h\tep\t7561\t7570\t7.4\t.\t.\tmult=7;src=W "1.05617;0.992;13:0"\n-chr2R\tw2h\tep\t7571\t7580\t9.7\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7581\t7590\t10.2\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t7591\t7600\t9\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7601\t7610\t9.7\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7611\t7620\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7621\t7630\t15.3\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t7631\t7640\t13.4\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7641\t7650\t13.7\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7651\t7660\t14.4\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t7661\t7670\t14.6\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t7671\t7680\t16.8\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7681\t7690\t16.7\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7691\t7700\t17.6\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t7701\t7710\t20.3\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7711\t7720\t20.5\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7721\t7730\t18.8\t.\t.\tmult=18;src=W "1.17304;0.992;35:0"\n-chr2R\tw2h\tep\t7731\t7740\t16.7\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7741\t7750\t16.8\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7751\t7760\t15.5\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t7761\t7770\t17.4\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t7771\t7780\t19.5\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7781\t7790\t19.1\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7791\t7800\t20.1\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7801\t7810\t22.7\t.\t.\tmult=22;src=W "1.21988;0.992;43:0"\n-chr2R\tw2h\tep\t7811\t7820\t24.4\t.\t.\tmult=24;src=W "1.24409;0.992;47:0"\n-chr2R\tw2h\tep\t7821\t7830\t23.6\t.\t.\tmult=23;src=W "1.23192;0.992;45:0"\n-chr2R\tw2h\tep\t7831\t7840\t19.5\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7841\t7850\t16.2\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7851\t7860\t14.8\t.\t.\tmult=14;src=W '..b'-chr2R\tw2h\tep\t8890\t8899\t15.3\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t8900\t8909\t17.6\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8910\t8919\t17.9\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8920\t8929\t17.2\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8930\t8939\t18.4\t.\t.\tmult=18;src=W "1.17304;0.992;35:0"\n-chr2R\tw2h\tep\t8940\t8949\t19.9\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t8950\t8959\t19.1\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t8960\t8969\t15.2\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t8970\t8979\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t8980\t8989\t14.7\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t8990\t8999\t14.5\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t9000\t9009\t14.5\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t9010\t9019\t12.5\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9020\t9029\t11.9\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t9030\t9039\t12.1\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9040\t9049\t10\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t9050\t9059\t9.7\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t9060\t9069\t10.6\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t9070\t9079\t12.3\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9080\t9089\t13.1\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t9090\t9099\t13.4\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t9100\t9109\t12\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9110\t9119\t10.7\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t9120\t9129\t11\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t9130\t9139\t10.9\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t9140\t9149\t7.9\t.\t.\tmult=7;src=W "1.05617;0.992;13:0"\n-chr2R\tw2h\tep\t9150\t9159\t4.9\t.\t.\tmult=4;src=W "1.02857;0.992;7:0"\n-chr2R\tw2h\tep\t9160\t9169\t4.4\t.\t.\tmult=4;src=W "1.02857;0.992;7:0"\n-chr2R\tw2h\tep\t9265\t9274\t11.4\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t9275\t9284\t12.8\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9285\t9294\t13.1\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t9295\t9304\t13.6\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t9305\t9314\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t9315\t9324\t12.4\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t9325\t9334\t9\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t9335\t9344\t5.2\t.\t.\tmult=5;src=W "1.03743;0.992;9:0"\n # Predicted genes for sequence number 1 on both strands\n # start gene chr2R.g1\n-chr2R\tAUGUSTUS\tgene\t7560\t9303\t0.79\t-\t.\tchr2R.g1\n-chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0.79\t-\t.\tchr2R.g1.t1\n+chr2R\tAUGUSTUS\tgene\t7560\t9303\t0.84\t-\t.\tchr2R.g1\n+chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0.84\t-\t.\tchr2R.g1.t1\n chr2R\tAUGUSTUS\tstart_codon\t9301\t9303\t.\t-\t0\ttranscript_id "chr2R.g1.t1"; gene_id "chr2R.g1";\n # Evidence for and against this transcript:\n # % of transcript supported by hints (any source): 57.1\n@@ -192,4 +58,4 @@\n # end gene chr2R.g1\n ###\n # command line:\n-# 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\n\\ No newline at end of file\n+# 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\n' |
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| 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 |
| b |
| b'@@ -1,17 +1,17 @@\n-# This output was generated with AUGUSTUS (version 3.2.3).\n+# This output was generated with AUGUSTUS (version 3.3.3).\n # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),\n-# O. Keller, S. K\xc3\xb6nig, L. Gerischer and L. Romoth.\n+# O. Keller, S. K\xc3\xb6nig, L. Gerischer, L. Romoth and Katharina Hoff.\n # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n # Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n # Sources of extrinsic information: M RM E W \n # Setting CDSpart local malus: 0.985\n # Setting UTRpart local malus: 0.973\n-# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat ...\n+# reading in the file /tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ...\n # Have extrinsic information about 1 sequences (in the specified range). \n-# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ...\n+# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...\n # fly version. Using default transition matrix.\n-# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat is in fasta format.\n+# Looks like /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat is in fasta format.\n # We have hints for 1 sequence and for 1 of the sequences in the input set.\n #\n # ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----\n@@ -34,120 +34,10 @@\n # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features\n # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features\n # Deleted 17 groups because some hint was not satisfiable.\n-# Constraints/Hints:\n-chr2R\tw2h\tep\t7551\t7560\t5.3\t.\t.\tmult=5;src=W "1.03743;0.992;9:0"\n-chr2R\tw2h\tep\t7561\t7570\t7.4\t.\t.\tmult=7;src=W "1.05617;0.992;13:0"\n-chr2R\tw2h\tep\t7571\t7580\t9.7\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7581\t7590\t10.2\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t7591\t7600\t9\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7601\t7610\t9.7\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t7611\t7620\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7621\t7630\t15.3\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t7631\t7640\t13.4\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7641\t7650\t13.7\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t7651\t7660\t14.4\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t7661\t7670\t14.6\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t7671\t7680\t16.8\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7681\t7690\t16.7\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7691\t7700\t17.6\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t7701\t7710\t20.3\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7711\t7720\t20.5\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7721\t7730\t18.8\t.\t.\tmult=18;src=W "1.17304;0.992;35:0"\n-chr2R\tw2h\tep\t7731\t7740\t16.7\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7741\t7750\t16.8\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7751\t7760\t15.5\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t7761\t7770\t17.4\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t7771\t7780\t19.5\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7781\t7790\t19.1\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7791\t7800\t20.1\t.\t.\tmult=20;src=W "1.19619;0.992;39:0"\n-chr2R\tw2h\tep\t7801\t7810\t22.7\t.\t.\tmult=22;src=W "1.21988;0.992;43:0"\n-chr2R\tw2h\tep\t7811\t7820\t24.4\t.\t.\tmult=24;src=W "1.24409;0.992;47:0"\n-chr2R\tw2h\tep\t7821\t7830\t23.6\t.\t.\tmult=23;src=W "1.23192;0.992;45:0"\n-chr2R\tw2h\tep\t7831\t7840\t19.5\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t7841\t7850\t16.2\t.\t.\tmult=16;src=W "1.15043;0.992;31:0"\n-chr2R\tw2h\tep\t7851\t7860\t14.8\t.\t.\tmult=14;src=W '..b'\tw2h\tep\t8370\t8379\t13.4\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t8380\t8389\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t8390\t8399\t11.8\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t8400\t8409\t9\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t8410\t8419\t7.7\t.\t.\tmult=7;src=W "1.05617;0.992;13:0"\n-chr2R\tw2h\tep\t8420\t8429\t8.9\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8430\t8439\t11.5\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t8440\t8449\t11.4\t.\t.\tmult=11;src=W "1.0964;0.992;21:0"\n-chr2R\tw2h\tep\t8450\t8459\t9.8\t.\t.\tmult=9;src=W "1.07589;0.992;17:0"\n-chr2R\tw2h\tep\t8460\t8469\t10.2\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t8470\t8479\t10.8\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t8480\t8489\t10\t.\t.\tmult=10;src=W "1.08606;0.992;19:0"\n-chr2R\tw2h\tep\t8490\t8499\t8.2\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8500\t8509\t7.1\t.\t.\tmult=7;src=W "1.05617;0.992;13:0"\n-chr2R\tw2h\tep\t8510\t8519\t4.2\t.\t.\tmult=4;src=W "1.02857;0.992;7:0"\n-chr2R\tw2h\tep\t8520\t8529\t4.7\t.\t.\tmult=4;src=W "1.02857;0.992;7:0"\n-chr2R\tw2h\tep\t8739\t8748\t4.3\t.\t.\tmult=4;src=W "1.02857;0.992;7:0"\n-chr2R\tw2h\tep\t8749\t8758\t5.7\t.\t.\tmult=5;src=W "1.03743;0.992;9:0"\n-chr2R\tw2h\tep\t8759\t8768\t8\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8769\t8778\t8\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8779\t8788\t8.6\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8789\t8798\t8.7\t.\t.\tmult=8;src=W "1.06592;0.992;15:0"\n-chr2R\tw2h\tep\t8880\t8889\t12.7\t.\t.\tmult=12;src=W "1.1069;0.992;23:0"\n-chr2R\tw2h\tep\t8890\t8899\t15.3\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t8900\t8909\t17.6\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8910\t8919\t17.9\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8920\t8929\t17.2\t.\t.\tmult=17;src=W "1.16167;0.992;33:0"\n-chr2R\tw2h\tep\t8930\t8939\t18.4\t.\t.\tmult=18;src=W "1.17304;0.992;35:0"\n-chr2R\tw2h\tep\t8940\t8949\t19.9\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t8950\t8959\t19.1\t.\t.\tmult=19;src=W "1.18455;0.992;37:0"\n-chr2R\tw2h\tep\t8960\t8969\t15.2\t.\t.\tmult=15;src=W "1.13933;0.992;29:0"\n-chr2R\tw2h\tep\t8970\t8979\t13\t.\t.\tmult=13;src=W "1.11756;0.992;25:0"\n-chr2R\tw2h\tep\t8980\t8989\t14.7\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t8990\t8999\t14.5\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n-chr2R\tw2h\tep\t9000\t9009\t14.5\t.\t.\tmult=14;src=W "1.12838;0.992;27:0"\n # Predicted genes for sequence number 1 on both strands\n # start gene chr2R.g1\n-chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.83\t-\t.\tchr2R.g1\n-chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.83\t-\t.\tchr2R.g1.t1\n+chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.84\t-\t.\tchr2R.g1\n+chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.84\t-\t.\tchr2R.g1.t1\n chr2R\tAUGUSTUS\tstart_codon\t8929\t8931\t.\t-\t0\ttranscript_id "chr2R.g1.t1"; gene_id "chr2R.g1";\n # Evidence for and against this transcript:\n # % of transcript supported by hints (any source): 60\n@@ -162,4 +52,4 @@\n # end gene chr2R.g1\n ###\n # command line:\n-# 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\n\\ No newline at end of file\n+# 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\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |