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comparison test-data/augustus.hints.output.gtf @ 5:7be22100e5e1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
author iuc
date Thu, 15 Jul 2021 17:16:33 +0000
parents 6519ebe25019
children
comparison
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4:6519ebe25019 5:7be22100e5e1
1 # This output was generated with AUGUSTUS (version 3.3.3). 1 # This output was generated with AUGUSTUS (version 3.4.0).
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 and Katharina Hoff.
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/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat ... 10 # reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.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 /home/abretaud/miniconda3/envs/__augustus@3.3.3/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/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat is in fasta format. 14 # Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.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
50 # CDS exons: 4/4 50 # CDS exons: 4/4
51 # W: 4 51 # W: 4
52 # CDS introns: 0/3 52 # CDS introns: 0/3
53 # 5'UTR exons and introns: 0/0 53 # 5'UTR exons and introns: 0/0
54 # 3'UTR exons and introns: 0/0 54 # 3'UTR exons and introns: 0/0
55 # hint groups fully obeyed: 0 55 # hint groups fully obeyed: 120
56 # incompatible hint groups: 129 56 # W: 120
57 # W: 129 57 # incompatible hint groups: 9
58 # W: 9
58 # end gene chr2R.g1 59 # end gene chr2R.g1
59 ### 60 ###
60 # command line: 61 # command line:
61 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/8/9/2/dataset_8920e51c-dd38-4e36-abf4-14825237cd41.dat --species=fly 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