Mercurial > repos > bgruening > augustus_training

comparison test-data/human_augustus_utr-on.gtf @ 4:6519ebe25019 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
author iuc
date Fri, 20 Dec 2019 14:09:14 -0500
parents 86c89c3bd99d
children 7be22100e5e1
comparison
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3:ccf8d0bbebe9 4:6519ebe25019
1 # This output was generated with AUGUSTUS (version 3.2.3). 1 # This output was generated with AUGUSTUS (version 3.3.3).
2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
3 # O. Keller, S. König, L. Gerischer and L. Romoth. 3 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7 # No extrinsic information on sequences given. 7 # No extrinsic information on sequences given.
8 # Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... 8 # Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
9 # human version. Using default transition matrix. 9 # human version. Using default transition matrix.
10 # Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat is in fasta format. 10 # Looks like /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat is in fasta format.
11 # We have hints for 0 sequences and for 0 of the sequences in the input set. 11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
12 # 12 #
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
14 # 14 #
15 # Constraints/Hints:
16 # (none)
17 # Predicted genes for sequence number 1 on both strands 15 # Predicted genes for sequence number 1 on both strands
18 # start gene HS04636.g1 16 # start gene HS04636.g1
19 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1 17 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1
20 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1 18 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1
21 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 19 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
70 # end gene HS04636.g1 68 # end gene HS04636.g1
71 ### 69 ###
72 # 70 #
73 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 71 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
74 # 72 #
75 # Constraints/Hints:
76 # (none)
77 # Predicted genes for sequence number 2 on both strands 73 # Predicted genes for sequence number 2 on both strands
78 # start gene HS08198.g2 74 # start gene HS08198.g2
79 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2 75 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2
80 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1 76 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1
81 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 77 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
104 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF 100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
105 # HVLDGECTAGASMAAW] 101 # HVLDGECTAGASMAAW]
106 # end gene HS08198.g2 102 # end gene HS08198.g2
107 ### 103 ###
108 # command line: 104 # command line:
109 # 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 105 # 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