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comparison test-data/human_augustus_utr-on.gtf @ 0:fcdd4f5c6cfc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Fri, 20 Oct 2017 03:48:35 -0400
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-1:000000000000 0:fcdd4f5c6cfc
1 # This output was generated with AUGUSTUS (version 3.2.3).
2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
3 # O. Keller, S. König, L. Gerischer and L. Romoth.
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
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7 # No extrinsic information on sequences given.
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 default transition matrix.
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.
12 #
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
14 #
15 # Constraints/Hints:
16 # (none)
17 # Predicted genes for sequence number 1 on both strands
18 # start gene HS04636.g1
19 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1
20 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1
21 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.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 "HS04636.g1.t1"; gene_id "HS04636.g1";
42 HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
43 HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.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]
63 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
64 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
65 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
66 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
67 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
68 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
69 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
70 # end gene HS04636.g1
71 ###
72 #
73 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
74 #
75 # Constraints/Hints:
76 # (none)
77 # Predicted genes for sequence number 2 on both strands
78 # start gene HS08198.g2
79 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2
80 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1
81 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
82 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
83 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
84 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
85 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
86 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
87 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
88 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
89 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
90 HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
91 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.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]
103 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
104 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
105 # HVLDGECTAGASMAAW]
106 # end gene HS08198.g2
107 ###
108 # command line:
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