# HG changeset patch
# User iuc
# Date 1626369393 0
# Node ID 7be22100e5e1799984614e5be9fd86e78102ca2b
# Parent 6519ebe25019577b19671b884475948485b121fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
diff -r 6519ebe25019 -r 7be22100e5e1 extract_features.py
--- a/extract_features.py Fri Dec 20 14:09:14 2019 -0500
+++ b/extract_features.py Thu Jul 15 17:16:33 2021 +0000
@@ -5,76 +5,88 @@
import textwrap
-def main( args ):
+def main(args):
"""
- Extract the protein and coding section from an augustus gff, gtf file
- Example file:
-HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
-HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
-# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
-# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
-# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
-# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
-# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
-# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
-# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
-# end gene g1
-###
-#
-# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
-#
-# Predicted genes for sequence number 2 on both strands
-# start gene g2
-HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
-HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
-HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
-HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
-HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
+ Extract the protein and coding section from an augustus gff, gtf file
+ Example file:
+ HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
+ HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
+ # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+ # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+ # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+ # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+ # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+ # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+ # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+ # end gene g1
+ ###
+ #
+ # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+ #
+ # Predicted genes for sequence number 2 on both strands
+ # start gene g2
+ HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
+ HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
+ HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
+ HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
+ HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
"""
- protein_seq = ''
- coding_seq = ''
+ protein_seq = ""
+ coding_seq = ""
if args.protein:
- po = open( args.protein, 'w+' )
+ po = open(args.protein, "w+")
if args.codingseq:
- co = open( args.codingseq, 'w+' )
+ co = open(args.codingseq, "w+")
for line in sys.stdin:
# protein- and coding-sequence are stored as comments
- if line.startswith('#'):
+ if line.startswith("#"):
line = line[2:].strip()
- if line.startswith('start gene'):
+ if line.startswith("start gene"):
gene_name = line[11:].strip()
if protein_seq:
- if line.endswith(']'):
+ if line.endswith("]"):
protein_seq += line[:-1]
- po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
- protein_seq = ''
+ po.write(
+ ">%s\n%s\n"
+ % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
+ )
+ protein_seq = ""
else:
protein_seq += line
if coding_seq:
- if line.endswith(']'):
+ if line.endswith("]"):
coding_seq += line[:-1]
- co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
- coding_seq = ''
+ co.write(
+ ">%s\n%s\n"
+ % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
+ )
+ coding_seq = ""
else:
coding_seq += line
- if args.protein and line.startswith('protein sequence = ['):
- if line.endswith(']'):
+ if args.protein and line.startswith("protein sequence = ["):
+ if line.endswith("]"):
protein_seq = line[20:-1]
- po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
- protein_seq = ''
+ po.write(
+ ">%s\n%s\n"
+ % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
+ )
+ protein_seq = ""
else:
line = line[20:]
protein_seq = line
- if args.codingseq and line.startswith('coding sequence = ['):
- if line.endswith(']'):
+ if args.codingseq and line.startswith("coding sequence = ["):
+ if line.endswith("]"):
coding_seq = line[19:-1]
- co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
- coding_seq = ''
+ co.write(
+ ">%s\n%s\n"
+ % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
+ )
+ coding_seq = ""
else:
line = line[19:]
coding_seq = line
@@ -85,10 +97,10 @@
po.close()
-if __name__ == '__main__':
+if __name__ == "__main__":
parser = argparse.ArgumentParser()
- parser.add_argument('-p', '--protein', help='Path to the protein file.')
- parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
+ parser.add_argument("-p", "--protein", help="Path to the protein file.")
+ parser.add_argument("-c", "--codingseq", help="Path to the coding file.")
args = parser.parse_args()
- main( args )
+ main(args)
diff -r 6519ebe25019 -r 7be22100e5e1 macros.xml
--- a/macros.xml Fri Dec 20 14:09:14 2019 -0500
+++ b/macros.xml Thu Jul 15 17:16:33 2021 +0000
@@ -7,7 +7,9 @@
- 3.3.3
+ 3.4.0
+ 0
+
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/augustus.hints.output.gtf
--- a/test-data/augustus.hints.output.gtf Fri Dec 20 14:09:14 2019 -0500
+++ b/test-data/augustus.hints.output.gtf Thu Jul 15 17:16:33 2021 +0000
@@ -1,4 +1,4 @@
-# This output was generated with AUGUSTUS (version 3.3.3).
+# 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),
@@ -7,11 +7,11 @@
# 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/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat ...
+# reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ...
# Have extrinsic information about 1 sequences (in the specified range).
-# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
+# Initializing the parameters using config directory /usr/local/config/ ...
# fly version. Using default transition matrix.
-# Looks like /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat is in fasta format.
+# Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.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) -----
@@ -52,10 +52,11 @@
# CDS introns: 0/3
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
-# hint groups fully obeyed: 0
-# incompatible hint groups: 129
-# W: 129
+# hint groups fully obeyed: 120
+# W: 120
+# incompatible hint groups: 9
+# W: 9
# 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/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/8/9/2/dataset_8920e51c-dd38-4e36-abf4-14825237cd41.dat --species=fly
+# 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
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/augustus.hints_and_range.output.gtf
--- a/test-data/augustus.hints_and_range.output.gtf Fri Dec 20 14:09:14 2019 -0500
+++ b/test-data/augustus.hints_and_range.output.gtf Thu Jul 15 17:16:33 2021 +0000
@@ -1,4 +1,4 @@
-# This output was generated with AUGUSTUS (version 3.3.3).
+# 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),
@@ -7,11 +7,11 @@
# 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/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ...
+# 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 /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
+# Initializing the parameters using config directory /usr/local/config/ ...
# fly version. Using default transition matrix.
-# Looks like /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat is in fasta format.
+# 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) -----
@@ -46,10 +46,11 @@
# CDS introns: 0/2
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
-# hint groups fully obeyed: 0
-# incompatible hint groups: 102
-# W: 102
+# 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/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/1/1/0/dataset_1106f730-ecae-4b8f-917b-47cb5fc7334d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly
+# 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
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/human_augustus_protein_codingseq_introns_cds_main.gtf
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri Dec 20 14:09:14 2019 -0500
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu Jul 15 17:16:33 2021 +0000
@@ -1,13 +1,13 @@
-# This output was generated with AUGUSTUS (version 3.3.3).
+# 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
# No extrinsic information on sequences given.
-# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
+# Initializing the parameters using config directory /usr/local/config/ ...
# human version. Using default transition matrix.
-# Looks like /tmp/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.dat is in fasta format.
+# Looks like /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.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) -----
@@ -98,4 +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/tmpTS0N1X/files/b/e/5/dataset_be5ee0f6-7fb0-4170-9543-17032878de48.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/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat --UTR=off --genemodel=complete --softmasking=0 --species=human
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/human_augustus_utr-on.gff
--- a/test-data/human_augustus_utr-on.gff Fri Dec 20 14:09:14 2019 -0500
+++ b/test-data/human_augustus_utr-on.gff Thu Jul 15 17:16:33 2021 +0000
@@ -1,14 +1,14 @@
##gff-version 3
-# This output was generated with AUGUSTUS (version 3.3.3).
+# 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
# No extrinsic information on sequences given.
-# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
+# Initializing the parameters using config directory /usr/local/config/ ...
# human version. Using default transition matrix.
-# Looks like /tmp/tmpTS0N1X/files/c/2/9/dataset_c29ecb21-0612-4152-8d35-994815171865.dat is in fasta format.
+# Looks like /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.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) -----
@@ -103,4 +103,4 @@
# end gene HS08198.g2
###
# command line:
-# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/c/2/9/dataset_c29ecb21-0612-4152-8d35-994815171865.dat --UTR=on --genemodel=complete --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/human_augustus_utr-on.gtf
--- a/test-data/human_augustus_utr-on.gtf Fri Dec 20 14:09:14 2019 -0500
+++ b/test-data/human_augustus_utr-on.gtf Thu Jul 15 17:16:33 2021 +0000
@@ -1,13 +1,13 @@
-# This output was generated with AUGUSTUS (version 3.3.3).
+# 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
# No extrinsic information on sequences given.
-# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
+# Initializing the parameters using config directory /usr/local/config/ ...
# human version. Using default transition matrix.
-# Looks like /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat is in fasta format.
+# Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.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) -----
@@ -102,4 +102,4 @@
# end gene HS08198.g2
###
# command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpTS0N1X/files/7/3/d/dataset_73d41293-49eb-4cbc-b881-ddc4c9faf952.dat --UTR=on --genemodel=complete --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
diff -r 6519ebe25019 -r 7be22100e5e1 test-data/human_augustus_utr-on_softmasking.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on_softmasking.gtf Thu Jul 15 17:16:33 2021 +0000
@@ -0,0 +1,24 @@
+# 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
+# No extrinsic information on sequences given.
+# Sources of extrinsic information: M RM
+# Initializing the parameters using config directory /usr/local/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.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) -----
+#
+# Predicted genes for sequence number 1 on both strands
+# (none)
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# (none)
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat --UTR=on --genemodel=complete --softmasking=1 --species=human