Mercurial > repos > bgruening > augustus
comparison test-data/augustus.hints.output.gtf @ 7:09855551d713 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
author | iuc |
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date | Thu, 15 Jul 2021 17:16:12 +0000 |
parents | ca6d970d931c |
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6:ca6d970d931c | 7:09855551d713 |
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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 |