Mercurial > repos > bgruening > augustus

comparison test-data/human_augustus_utr-on.gtf @ 3:f5075dee9d6b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
author iuc
date Fri, 22 May 2015 04:55:25 -0400
parents af307d3285c5
children 4de31938431b
comparison
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2:a77a4e9921e0 3:f5075dee9d6b
1 # This output was generated with AUGUSTUS (version 2.7). 1 # This output was generated with AUGUSTUS (version 3.1.0).
2 # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de) 2 # AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
3 # and Oliver Keller (keller@cs.uni-goettingen.de). 3 # Oliver Keller, Stefanie König and Lizzy Gerischer.
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 ... 8 # Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
9 # human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl 9 # human version. Using default transition matrix.
10 # Looks like ./examples/example.fa is in fasta format. 10 # Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.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: 15 # Constraints/Hints:
16 # (none) 16 # (none)
17 # Predicted genes for sequence number 1 on both strands 17 # Predicted genes for sequence number 1 on both strands
18 # start gene g1 18 # start gene HS04636.g1
19 HS04636 AUGUSTUS gene 836 8857 1 + . g1 19 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1
20 HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 20 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1
21 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; 21 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
22 HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; 22 HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
23 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 23 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
24 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 24 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
25 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 25 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
26 HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; 26 HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
27 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 27 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
28 HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; 28 HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
29 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 29 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
30 HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; 30 HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
31 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 31 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
32 HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; 32 HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
33 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 33 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
34 HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; 34 HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
35 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 35 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
36 HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; 36 HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
37 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 37 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
38 HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; 38 HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
39 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 39 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
40 HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; 40 HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
41 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; 41 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
42 HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 42 HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
43 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; 43 HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
44 HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 44 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
45 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
46 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
47 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
48 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
49 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
50 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
51 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
52 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
53 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
54 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
55 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
56 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
57 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
58 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
59 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
60 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
61 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
62 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
45 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 63 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
46 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 64 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
47 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 65 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
48 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 66 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
49 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 67 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
50 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV 68 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
51 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] 69 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
52 # end gene g1 70 # end gene HS04636.g1
53 ### 71 ###
54 # 72 #
55 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 73 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
56 # 74 #
57 # Constraints/Hints: 75 # Constraints/Hints:
58 # (none) 76 # (none)
59 # Predicted genes for sequence number 2 on both strands 77 # Predicted genes for sequence number 2 on both strands
60 # start gene g2 78 # start gene HS08198.g2
61 HS08198 AUGUSTUS gene 86 2344 1 + . g2 79 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2
62 HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 80 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1
63 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; 81 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
64 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; 82 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
65 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 83 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
66 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 84 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
67 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 85 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
68 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; 86 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
69 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 87 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
70 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; 88 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
71 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 89 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
72 HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; 90 HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
73 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 91 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
74 HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; 92 HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
93 HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
94 HS08198 AUGUSTUS exon 1772 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
95 HS08198 AUGUSTUS tts 2105 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
96 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
97 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
98 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
99 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
100 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
101 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
102 # ggcgtggtga]
75 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC 103 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
76 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] 104 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
77 # end gene g2 105 # HVLDGECTAGASMAAW]
106 # end gene HS08198.g2
78 ### 107 ###
79 # command line: 108 # command line:
80 # ./bin/augustus --species=human --UTR=on ./examples/example.fa 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