Mercurial > repos > bgruening > augustus_training

comparison test-data/human_augustus_protein_codingseq_introns_cds_main.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/000/6/task_0/dataset_9.dat is in fasta format. 10 # Looks like /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.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 966 6903 1 + . HS04636.g1 17 HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1
20 HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1 18 HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1
21 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 19 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
68 # end gene HS04636.g1 66 # end gene HS04636.g1
69 ### 67 ###
70 # 68 #
71 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 69 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
72 # 70 #
73 # Constraints/Hints:
74 # (none)
75 # Predicted genes for sequence number 2 on both strands 71 # Predicted genes for sequence number 2 on both strands
76 # start gene HS08198.g2 72 # start gene HS08198.g2
77 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2 73 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2
78 HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1 74 HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1
79 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 75 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF 96 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
101 # HVLDGECTAGASMAAW] 97 # HVLDGECTAGASMAAW]
102 # end gene HS08198.g2 98 # end gene HS08198.g2
103 ### 99 ###
104 # command line: 100 # command line:
105 # 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 101 # 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