Mercurial > repos > bgruening > augustus_training

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
equal deleted inserted replaced
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/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ... 10 # reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.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/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat is in fasta format. 14 # Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.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 = 2001, name = chr2R) ----- 17 # ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
18 # 18 #
19 # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features 19 # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
44 # CDS exons: 3/3 44 # CDS exons: 3/3
45 # W: 3 45 # W: 3
46 # CDS introns: 0/2 46 # CDS introns: 0/2
47 # 5'UTR exons and introns: 0/0 47 # 5'UTR exons and introns: 0/0
48 # 3'UTR exons and introns: 0/0 48 # 3'UTR exons and introns: 0/0
49 # hint groups fully obeyed: 0 49 # hint groups fully obeyed: 96
50 # incompatible hint groups: 102 50 # W: 96
51 # W: 102 51 # incompatible hint groups: 6
52 # W: 6
52 # end gene chr2R.g1 53 # end gene chr2R.g1
53 ### 54 ###
54 # command line: 55 # command line:
55 # 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/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/1/1/0/dataset_1106f730-ecae-4b8f-917b-47cb5fc7334d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly 56 # 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/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/3/3/5/dataset_335e9fec-9340-42e6-97ce-af35d5220fcc.dat --predictionStart=7000 --predictionEnd=9000 --species=fly