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comparison test-data/human_augustus_utr-on.gff @ 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
equal deleted inserted replaced
2:a77a4e9921e0 3:f5075dee9d6b
1 ##gff-version 3 1 ##gff-version 3
2 # This output was generated with AUGUSTUS (version 2.7). 2 # This output was generated with AUGUSTUS (version 3.1.0).
3 # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de) 3 # AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
4 # and Oliver Keller (keller@cs.uni-goettingen.de). 4 # Oliver Keller, Stefanie König and Lizzy Gerischer.
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 # Initialising the parameters ... 9 # Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
10 # human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl 10 # human version. Using default transition matrix.
11 # Looks like ./examples/example.fa is in fasta format. 11 # Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.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 g1 17 # start gene HS04636.g1
18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1
19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1
20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1
21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1
22 HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 22 HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1
23 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 23 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
24 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 24 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
25 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 25 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1
26 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 26 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
27 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 27 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1
28 HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 28 HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
29 HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 29 HS04636 AUGUSTUS exon 2852 2995 . + . Parent=HS04636.g1.t1
30 HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 30 HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
31 HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 31 HS04636 AUGUSTUS exon 3426 3607 . + . Parent=HS04636.g1.t1
32 HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 32 HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
33 HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 33 HS04636 AUGUSTUS exon 4340 4423 . + . Parent=HS04636.g1.t1
34 HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 34 HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
35 HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 35 HS04636 AUGUSTUS exon 4543 4789 . + . Parent=HS04636.g1.t1
36 HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 36 HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
37 HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1 37 HS04636 AUGUSTUS exon 5072 5358 . + . Parent=HS04636.g1.t1
38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=g1.t1.cds;Parent=g1.t1 38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
39 HS04636 AUGUSTUS exon 5860 6007 . + . Parent=g1.t1 39 HS04636 AUGUSTUS exon 5860 6007 . + . Parent=HS04636.g1.t1
40 HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=g1.t1.cds;Parent=g1.t1 40 HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
41 HS04636 AUGUSTUS exon 6494 8857 . + . Parent=g1.t1 41 HS04636 AUGUSTUS exon 6494 8857 . + . Parent=HS04636.g1.t1
42 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1 42 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=HS04636.g1.t1
43 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1 43 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
44 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
45 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
46 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
47 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
48 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
49 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
50 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
51 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
52 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
53 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
54 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
55 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
56 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
57 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
58 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
59 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
60 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
61 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
44 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 62 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
45 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 63 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
46 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 64 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
47 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 65 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
48 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 66 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
49 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV 67 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
50 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] 68 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
51 # end gene g1 69 # end gene HS04636.g1
52 ### 70 ###
53 # 71 #
54 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 72 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
55 # 73 #
56 # Predicted genes for sequence number 2 on both strands 74 # Predicted genes for sequence number 2 on both strands
57 # start gene g2 75 # start gene HS08198.g2
58 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2 76 HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2
59 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2 77 HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2
60 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1 78 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1
61 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1 79 HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1
62 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1 80 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1
63 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=g2.t1.cds;Parent=g2.t1 81 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
64 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=g2.t1.cds;Parent=g2.t1 82 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
65 HS08198 AUGUSTUS exon 812 894 . + . Parent=g2.t1 83 HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1
66 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=g2.t1.cds;Parent=g2.t1 84 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
67 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=g2.t1 85 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1
68 HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=g2.t1.cds;Parent=g2.t1 86 HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
69 HS08198 AUGUSTUS exon 1208 1315 . + . Parent=g2.t1 87 HS08198 AUGUSTUS exon 1208 1315 . + . Parent=HS08198.g2.t1
70 HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=g2.t1.cds;Parent=g2.t1 88 HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
71 HS08198 AUGUSTUS exon 1587 1688 . + . Parent=g2.t1 89 HS08198 AUGUSTUS exon 1587 1688 . + . Parent=HS08198.g2.t1
90 HS08198 AUGUSTUS CDS 1772 1848 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
91 HS08198 AUGUSTUS exon 1772 2105 . + . Parent=HS08198.g2.t1
92 HS08198 AUGUSTUS transcription_end_site 2105 2105 . + . Parent=HS08198.g2.t1
93 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
94 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
95 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
96 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
97 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
98 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
99 # ggcgtggtga]
72 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC 100 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
73 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] 101 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
74 # end gene g2 102 # HVLDGECTAGASMAAW]
103 # end gene HS08198.g2
75 ### 104 ###
76 # command line: 105 # command line:
77 # ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa 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/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human