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comparison test-data/human_augustus_protein_codingseq_introns_cds_main.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/000/6/task_0/dataset_9.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 966 6903 1 + . HS04636.g1
20 HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1
21 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
22 HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
23 HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
24 HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
25 HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
26 HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
27 HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
28 HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
29 HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
30 HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
31 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
32 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
33 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
34 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
35 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
36 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
37 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
38 HS04636 AUGUSTUS CDS 5072 5358 . + 2 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 CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
41 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
42 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
43 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
44 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
45 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
46 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
47 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
48 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
49 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
50 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
51 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
52 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
53 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
54 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
55 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
56 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
57 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
58 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
59 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
60 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
61 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
62 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
63 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
64 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
65 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
66 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
67 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
68 # end gene HS04636.g1
69 ###
70 #
71 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
72 #
73 # Constraints/Hints:
74 # (none)
75 # Predicted genes for sequence number 2 on both strands
76 # start gene HS08198.g2
77 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2
78 HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1
79 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
80 HS08198 AUGUSTUS intron 583 811 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
81 HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
82 HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
83 HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
84 HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
85 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
86 HS08198 AUGUSTUS CDS 812 894 . + 0 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 CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
89 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
90 HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
91 HS08198 AUGUSTUS stop_codon 1846 1848 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
92 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
93 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
94 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
95 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
96 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
97 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
98 # ggcgtggtga]
99 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
101 # HVLDGECTAGASMAAW]
102 # end gene HS08198.g2
103 ###
104 # command line:
105 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human