# 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 /augustus/config/ ...
# Using protein profile unknown
# --[0..49]--> unknown_A (151) <--[0..0]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig114020180911_busco_2432604931_.temp 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 = 20422, name = Contig1140) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1140	AUGUSTUS	gene	15975	19742	0.62	-	.	g1
Contig1140	AUGUSTUS	transcript	15975	19742	0.62	-	.	g1.t1
Contig1140	AUGUSTUS	stop_codon	15975	15977	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1140	AUGUSTUS	intron	16341	19433	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1140	AUGUSTUS	CDS	15975	16340	0.76	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1140	AUGUSTUS	CDS	19434	19742	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1140	AUGUSTUS	start_codon	19740	19742	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgataacacccattcttcaaaatccttcatttacgtttcctcatccattgggaataaatctccagtctgcttccagtg
# tacctcctactgttcctgtggcagctaacattgtatcaaatgtaggtcaaggtgggtccctacctatacaaccaattttggtatcaggtggacaacag
# gtatccacgtcatcagaatctaccggtgttccggatcctgttaccacagcagtgaagcaggaaactccatcaacaaacacacccactggttctcacaa
# cactggagcagatgacaaggaaacagatgaaaaggtgatctcccaactatcagctggattagtgcctcatgttgtacgggagtggcgcctagtcaatc
# caaagcgaactcgcgtatcttttgagcatgcgtctagtgcgagagagagtcggtcttatgcaaagaacgaatgggtagagaaagagaccgcggcagtt
# cgcttatcatcccccacgctgctacctgcaaggatcgaccaccggcaactggtcacctgccctatctctgaccccgctcacagtatgtccaatgctcg
# ccaacgttgtcacgccttagatgcaacaccacgcgaagaggactctcacggcctcacatgcttttactctcgcgcgcctgtctccccgtttaacatag
# atacatag]
# protein sequence = [MITPILQNPSFTFPHPLGINLQSASSVPPTVPVAANIVSNVGQGGSLPIQPILVSGGQQVSTSSESTGVPDPVTTAVK
# QETPSTNTPTGSHNTGADDKETDEKVISQLSAGLVPHVVREWRLVNPKRTRVSFEHASSARESRSYAKNEWVEKETAAVRLSSPTLLPARIDHRQLVT
# CPISDPAHSMSNARQRCHALDATPREEDSHGLTCFYSRAPVSPFNIDT]
# end gene g1
###
# start gene g2
Contig1140	AUGUSTUS	gene	19945	21380	0.37	-	.	g2
Contig1140	AUGUSTUS	transcript	19945	21380	0.37	-	.	g2.t1
Contig1140	AUGUSTUS	stop_codon	19945	19947	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	intron	20515	20948	0.98	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	intron	21020	21325	0.43	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	CDS	19945	20514	0.97	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	CDS	20949	21019	0.98	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	CDS	21326	21380	0.37	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig1140	AUGUSTUS	start_codon	21378	21380	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtttgaattgagtagagatgaacacagtatttgtttgtcttttgttcggtatgttgatgaaggagcggagtctgttg
# atgatgactcaagtaatgacagttaccgtgacccagcaagtgaagaggagggtgatataaaacaggaaccaaatgtcttggattacactgtacaagct
# gctgaaagcactcatcaaacaggagatcacctgctcccactgtgtacagactcaggaggagataacctttcacaagcaataccaatggtcaaacaaga
# accgacagacaatggtgaatatgggaattctgtgatacaaagtgtagagaccactcacacaaagactgtttctattgatcatacacagcttacatcat
# caggtgccgcgtctcatcccgtcatgtcagatcccaatgtaggagttgtgaaacaagaaccagtagacagtggtgaatgtgagagttctgtgtcaaaa
# tgtgtatcaactatagagaggtctgtttctcatcatagttcatctccatcatccagtgcttcagtactgaagccagccatgtcgaataacattgttac
# atcatccagtgcccccgcctcattttctgtcgtgccaactaacactgttacttccgtcaaatcttcagtgattcagggaattccctccaccgtaaaca
# gctttatgggacaggacaccaacctctga]
# protein sequence = [MFELSRDEHSICLSFVRYVDEGAESVDDDSSNDSYRDPASEEEGDIKQEPNVLDYTVQAAESTHQTGDHLLPLCTDSG
# GDNLSQAIPMVKQEPTDNGEYGNSVIQSVETTHTKTVSIDHTQLTSSGAASHPVMSDPNVGVVKQEPVDSGECESSVSKCVSTIERSVSHHSSSPSSS
# ASVLKPAMSNNIVTSSSAPASFSVVPTNTVTSVKSSVIQGIPSTVNSFMGQDTNL]
# end gene g2
###
# start gene g3
Contig1140	AUGUSTUS	gene	28023	28450	0.28	+	.	g3
Contig1140	AUGUSTUS	transcript	28023	28450	0.28	+	.	g3.t1
Contig1140	AUGUSTUS	start_codon	28023	28025	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig1140	AUGUSTUS	intron	28200	28450	0.45	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig1140	AUGUSTUS	CDS	28023	28199	0.6	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgacaggtgtcatccttcgtgactcccacggtgtggcccaagtccgctttgtcacaggtaacaaaattctgaggattc
# tgaagaaaaagggcatggcccccgatcttcctgaggatctgtatcatcttatcaagaaggctgtcaacatcagaaaacacatggaaaggaacaggaag]
# protein sequence = [MTGVILRDSHGVAQVRFVTGNKILRILKKKGMAPDLPEDLYHLIKKAVNIRKHMERNRK]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370Y63.prfl --predictionStart=8029  --predictionEnd=48199  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig114020180911_busco_2432604931_.temp