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comparison test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 7:09855551d713 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 17:16:12 +0000
parents ca6d970d931c
children
comparison
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6:ca6d970d931c 7:09855551d713
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 # No extrinsic information on sequences given. 7 # No extrinsic information on sequences given.
8 # Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... 8 # Initializing the parameters using config directory /usr/local/config/ ...
9 # human version. Using default transition matrix. 9 # human version. Using default transition matrix.
10 # Looks like /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat is in fasta format. 10 # Looks like /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat is in fasta format.
11 # We have hints for 0 sequences and for 0 of the sequences in the input set. 11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
12 # 12 #
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
14 # 14 #
15 # Predicted genes for sequence number 1 on both strands 15 # Predicted genes for sequence number 1 on both strands
96 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF 96 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
97 # HVLDGECTAGASMAAW] 97 # HVLDGECTAGASMAAW]
98 # end gene HS08198.g2 98 # end gene HS08198.g2
99 ### 99 ###
100 # command line: 100 # command line:
101 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat --UTR=off --genemodel=complete --species=human 101 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat --UTR=off --genemodel=complete --softmasking=0 --species=human