comparison test-data/augustus.hints_and_range.output.gtf @ 11:534814b64234 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782

10:0fc0f9cf035a

# This output was generated with AUGUSTUS (version 3.4.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# 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

# 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

# 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

11:534814b64234

# This output was generated with AUGUSTUS (version 3.5.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# 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/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.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/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.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

# 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
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 60
# CDS exons: 3/3
#      W:   3 
# CDS introns: 0/2

# 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 --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/7/6/7/dataset_7673297f-b12d-48f2-b40c-2fcd8e18239d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly