Mercurial > repos > bgruening > augustus
comparison test-data/human_augustus_utr-on.gtf @ 7:09855551d713 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
author | iuc |
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date | Thu, 15 Jul 2021 17:16:12 +0000 |
parents | ca6d970d931c |
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6:ca6d970d931c | 7:09855551d713 |
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1 # This output was generated with AUGUSTUS (version 3.3.3). | 1 # This output was generated with AUGUSTUS (version 3.4.0). |
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, L. Romoth and Katharina Hoff. | 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 # Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... | 8 # Initializing the parameters using config directory /usr/local/config/ ... |
9 # human version. Using default transition matrix. | 9 # human version. Using default transition matrix. |
10 # Looks like /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat is in fasta format. | 10 # Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.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 # Predicted genes for sequence number 1 on both strands | 15 # Predicted genes for sequence number 1 on both strands |
100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF | 100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF |
101 # HVLDGECTAGASMAAW] | 101 # HVLDGECTAGASMAAW] |
102 # end gene HS08198.g2 | 102 # end gene HS08198.g2 |
103 ### | 103 ### |
104 # command line: | 104 # command line: |
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 | 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/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human |