Mercurial > repos > bgruening > augustus_training

comparison test-data/human_augustus_utr-on.gtf @ 9:2fdc599f2814 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
author iuc
date Thu, 17 Jul 2025 09:06:11 +0000
parents 7be22100e5e1
children
comparison
equal deleted inserted replaced
8:aada0deea587 9:2fdc599f2814
1 # This output was generated with AUGUSTUS (version 3.4.0). 1 # Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat is in gzip format. Deflating...
2 # This output was generated with AUGUSTUS (version 3.5.0).
2 # 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),
3 # 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.
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 5 # 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 6 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 7 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7 # No extrinsic information on sequences given. 8 # No extrinsic information on sequences given.
8 # Initializing the parameters using config directory /usr/local/config/ ... 9 # Initializing the parameters using config directory /usr/local/config/ ...
9 # human version. Using default transition matrix. 10 # human version. Using default transition matrix.
10 # Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat is in fasta format. 11 # Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat is in fasta format.
11 # 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.
12 # 13 #
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
14 # 15 #
15 # Predicted genes for sequence number 1 on both strands 16 # Predicted genes for sequence number 1 on both strands
16 # start gene HS04636.g1 17 # start gene HS04636.g1
17 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1 18 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1
18 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1 19 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1
19 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 20 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
20 HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 21 HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
21 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
22 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 22 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
23 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 23 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
24 HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 24 HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
25 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 25 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
26 HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; 26 HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
74 # start gene HS08198.g2 74 # start gene HS08198.g2
75 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2 75 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2
76 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1 76 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1
77 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";
78 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 78 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
79 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
80 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 79 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
81 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 80 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
82 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 81 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
83 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 82 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
84 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; 83 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF 99 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
101 # HVLDGECTAGASMAAW] 100 # HVLDGECTAGASMAAW]
102 # end gene HS08198.g2 101 # end gene HS08198.g2
103 ### 102 ###
104 # command line: 103 # 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/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human 104 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat --UTR=on --genemodel=complete --softmasking=0 --species=human