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comparison test-data/augustus.hints.output.gtf @ 11:534814b64234 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 09:06:01 +0000
parents 09855551d713
children
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10:0fc0f9cf035a 11:534814b64234
1 # This output was generated with AUGUSTUS (version 3.4.0). 1 # 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), 2 # 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. 3 # 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), 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 # Sources of extrinsic information: M RM E W 7 # Sources of extrinsic information: M RM E W
8 # Setting CDSpart local malus: 0.985 8 # Setting CDSpart local malus: 0.985
9 # Setting UTRpart local malus: 0.973 9 # Setting UTRpart local malus: 0.973
10 # reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ... 10 # reading in the file /tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat ...
11 # Have extrinsic information about 1 sequences (in the specified range). 11 # Have extrinsic information about 1 sequences (in the specified range).
12 # Initializing the parameters using config directory /usr/local/config/ ... 12 # Initializing the parameters using config directory /usr/local/config/ ...
13 # fly version. Using default transition matrix. 13 # fly version. Using default transition matrix.
14 # Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat is in fasta format. 14 # Looks like /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat is in fasta format.
15 # We have hints for 1 sequence and for 1 of the sequences in the input set. 15 # We have hints for 1 sequence and for 1 of the sequences in the input set.
16 # 16 #
17 # ----- prediction on sequence number 1 (length = 9950, name = chr2R) ----- 17 # ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
18 # 18 #
19 # Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features 19 # Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
42 # Deleted 23 groups because some hint was not satisfiable. 42 # Deleted 23 groups because some hint was not satisfiable.
43 # Predicted genes for sequence number 1 on both strands 43 # Predicted genes for sequence number 1 on both strands
44 # start gene chr2R.g1 44 # start gene chr2R.g1
45 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1 45 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1
46 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1 46 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1
47 chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
48 # Evidence for and against this transcript: 47 # Evidence for and against this transcript:
49 # % of transcript supported by hints (any source): 57.1 48 # % of transcript supported by hints (any source): 57.1
50 # CDS exons: 4/4 49 # CDS exons: 4/4
51 # W: 4 50 # W: 4
52 # CDS introns: 0/3 51 # CDS introns: 0/3
57 # incompatible hint groups: 9 56 # incompatible hint groups: 9
58 # W: 9 57 # W: 9
59 # end gene chr2R.g1 58 # end gene chr2R.g1
60 ### 59 ###
61 # command line: 60 # command line:
62 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/8/6/b/dataset_86b0a149-1d37-4615-9915-2c48586e3ca1.dat --species=fly 61 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/3/4/e/dataset_34e31244-f096-4c30-9f0d-5ca9e518e4bb.dat --species=fly