Mercurial > repos > bgruening > augustus_training
diff test-data/augustus.hints.output.gtf @ 9:2fdc599f2814 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
| author | iuc |
|---|---|
| date | Thu, 17 Jul 2025 09:06:11 +0000 |
| parents | 7be22100e5e1 |
| children |
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--- a/test-data/augustus.hints.output.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/augustus.hints.output.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # 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. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ... +# reading in the file /tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.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/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.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 = 9950, name = chr2R) ----- @@ -44,7 +44,6 @@ # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1 -chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 57.1 # CDS exons: 4/4 @@ -59,4 +58,4 @@ # 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/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 +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/3/4/e/dataset_34e31244-f096-4c30-9f0d-5ca9e518e4bb.dat --species=fly