Mercurial > repos > bgruening > augustus_training
diff test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 4:6519ebe25019 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
| author | iuc |
|---|---|
| date | Fri, 20 Dec 2019 14:09:14 -0500 |
| parents | 86c89c3bd99d |
| children | 7be22100e5e1 |
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--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu May 30 06:58:53 2019 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri Dec 20 14:09:14 2019 -0500 @@ -1,19 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.2.3). +# This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer and L. Romoth. +# 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 # No extrinsic information on sequences given. -# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format. +# Looks like /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 1 on both strands # start gene HS04636.g1 HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1 @@ -70,8 +68,6 @@ # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # -# Constraints/Hints: -# (none) # Predicted genes for sequence number 2 on both strands # start gene HS08198.g2 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2 @@ -102,4 +98,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human +# 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