Mercurial > repos > bgruening > augustus_training
comparison test-data/human_augustus_utr-on.gff @ 9:2fdc599f2814 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
author | iuc |
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date | Thu, 17 Jul 2025 09:06:11 +0000 |
parents | 7be22100e5e1 |
children |
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8:aada0deea587 | 9:2fdc599f2814 |
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1 ##gff-version 3 | 1 ##gff-version 3 |
2 # This output was generated with AUGUSTUS (version 3.4.0). | 2 # This output was generated with AUGUSTUS (version 3.5.0). |
3 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), | 3 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), |
4 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. | 4 # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. |
5 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), | 5 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), |
6 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding | 6 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding |
7 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 | 7 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 |
8 # No extrinsic information on sequences given. | 8 # No extrinsic information on sequences given. |
9 # Initializing the parameters using config directory /usr/local/config/ ... | 9 # Initializing the parameters using config directory /usr/local/config/ ... |
10 # human version. Using default transition matrix. | 10 # human version. Using default transition matrix. |
11 # Looks like /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat is in fasta format. | 11 # Looks like /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.dat is in fasta format. |
12 # We have hints for 0 sequences and for 0 of the sequences in the input set. | 12 # We have hints for 0 sequences and for 0 of the sequences in the input set. |
13 # | 13 # |
14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- | 14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- |
15 # | 15 # |
16 # Predicted genes for sequence number 1 on both strands | 16 # Predicted genes for sequence number 1 on both strands |
17 # start gene HS04636.g1 | 17 # start gene HS04636.g1 |
18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1 | 18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1 |
19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1 | 19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1 |
20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1 | 20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1 |
21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1 | 21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1 |
22 HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1 | |
23 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 | 22 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 |
24 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 | 23 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 |
25 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1 | 24 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1 |
26 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 | 25 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 |
27 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1 | 26 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1 |
75 # start gene HS08198.g2 | 74 # start gene HS08198.g2 |
76 HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2 | 75 HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2 |
77 HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2 | 76 HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2 |
78 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1 | 77 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1 |
79 HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1 | 78 HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1 |
80 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1 | |
81 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 | 79 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 |
82 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 | 80 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 |
83 HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1 | 81 HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1 |
84 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 | 82 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 |
85 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1 | 83 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1 |
101 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF | 99 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF |
102 # HVLDGECTAGASMAAW] | 100 # HVLDGECTAGASMAAW] |
103 # end gene HS08198.g2 | 101 # end gene HS08198.g2 |
104 ### | 102 ### |
105 # command line: | 103 # command line: |
106 # augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat --UTR=on --genemodel=complete --softmasking=0 --species=human | 104 # augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.dat --UTR=on --genemodel=complete --softmasking=0 --species=human |