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view test-data/augustus.hints_and_range.output.gtf @ 8:aada0deea587 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 69d542836dbce9261906bb0d1e7ef39f9712f4a3
author | iuc |
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date | Sun, 15 Dec 2024 09:09:49 +0000 |
parents | 7be22100e5e1 |
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# This output was generated with AUGUSTUS (version 3.4.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 # reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat ... # Have extrinsic information about 1 sequences (in the specified range). # Initializing the parameters using config directory /usr/local/config/ ... # fly version. Using default transition matrix. # Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 2001, name = chr2R) ----- # # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features # Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features # Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features # Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features # Deleted 17 groups because some hint was not satisfiable. # Predicted genes for sequence number 1 on both strands # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 8931 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1 chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 60 # CDS exons: 3/3 # W: 3 # CDS introns: 0/2 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 96 # W: 96 # incompatible hint groups: 6 # W: 6 # end gene chr2R.g1 ### # command line: # 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