# 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..58]--> unknown_A (24) <--[0..1]--> unknown_B (43) <--[6..12]--> unknown_C (60) <--[0..1]--> unknown_D (89) <--[0..1]--> unknown_E (19) <--[0..9]--> unknown_F (8) <--[0..26]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig620180911_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 = 24337, name = Contig6) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig6	AUGUSTUS	gene	71404	75775	0.12	-	.	g1
Contig6	AUGUSTUS	transcript	71404	75775	0.12	-	.	g1.t1
Contig6	AUGUSTUS	stop_codon	71404	71406	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig6	AUGUSTUS	intron	71644	75745	0.23	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig6	AUGUSTUS	CDS	71404	71643	0.29	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig6	AUGUSTUS	CDS	75746	75775	0.29	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig6	AUGUSTUS	start_codon	75773	75775	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctggagttcctcattgacaatatctttataaaaccaggagctcgggtggtcaggggaccggattgggaatcgaaga
# agcaggacagcggcgagggatttctgggtaccataatattcgtacccaaatctgggtcgaatgataacaaggtgacggtgatctgggactctggaata
# gagcgccgatacagagcgggccatcaaggaaagtacgaccttaaagtgtacgacacagctcccacgggtaacaaccttattatcatgctttaa]
# protein sequence = [MLEFLIDNIFIKPGARVVRGPDWESKKQDSGEGFLGTIIFVPKSGSNDNKVTVIWDSGIERRYRAGHQGKYDLKVYDT
# APTGNNLIIML]
# end gene g1
###
# start gene g2
Contig6	AUGUSTUS	gene	77213	77731	0.2	+	.	g2
Contig6	AUGUSTUS	transcript	77213	77731	0.2	+	.	g2.t1
Contig6	AUGUSTUS	start_codon	77213	77215	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig6	AUGUSTUS	intron	77340	77438	0.32	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig6	AUGUSTUS	CDS	77213	77339	0.35	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig6	AUGUSTUS	CDS	77439	77731	0.47	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig6	AUGUSTUS	stop_codon	77729	77731	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatagaacaccaaagagagatgtcaccattctgatgggcgatctcgacgcaaaagtggagagcaacaaccctggaa
# gggaactcatcatgggaaatcttgaacttgggaacatgaatgagaatgacctagcaaaagaaaaccaaatcgaccacctgacaatctcgcggcgatgg
# agaaggaccttgatggatgtcagagtatatagaggggctaacgtggtatcagaacactctttggtgattggaaaactgagagtgaaaatacaagcaat
# aaggaaaactggctctcaacgaaacccaaaattcgatgtcccaaaattcaagacaccaatccagaaagaggacttttccatctccctcaagaacagat
# tccaggcactcgctgatctgggggatggctcactagagaagaagtga]
# protein sequence = [MDRTPKRDVTILMGDLDAKVESNNPGRELIMGNLELGNMNENDLAKENQIDHLTISRRWRRTLMDVRVYRGANVVSEH
# SLVIGKLRVKIQAIRKTGSQRNPKFDVPKFKTPIQKEDFSISLKNRFQALADLGDGSLEKK]
# end gene g2
###
# start gene g3
Contig6	AUGUSTUS	gene	78357	79082	1	+	.	g3
Contig6	AUGUSTUS	transcript	78357	79082	1	+	.	g3.t1
Contig6	AUGUSTUS	start_codon	78357	78359	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig6	AUGUSTUS	CDS	78357	79082	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig6	AUGUSTUS	stop_codon	79080	79082	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgggagatatacctaaggagtggaggacaggctacattgtgaaagttccaaagaaaggagacctcattgactgccaga
# actggatagggatacagcttctttctttaccaagcaaagtcttcgccagggtgattctaaagacgaccaaagctacgattgacgctaccatgagagaa
# gagcaggcaggatttcggaccggaagatcatgtgctgatcagattgcaactctatgcttcatcattgagcaatcgctggagtggcagtcaccactgtt
# tgtcaactttgtggattttaaaaggacctttgatgtggtggatcaggtaccgatctggcaaatccttagacactatgacatccctcggaagattgtca
# gcatcatccagagcctctatagagacaccaactgcagcgtcatccacaacgctaacatatcaacatcctttgagattaacaccgtagtcaagcaaggg
# tgcctgttatcaccactaatcttctcaatggtgattgactgggtaattaaaaccattatgaatcaaccaagagccatcgaatggactacgatgaaaaa
# actcgaagaccttgatttcgccgatgacatcgtcctgttatcgcactctcatagacacatgcaagacaaaacagagaatctaaccaatgttgccaaga
# ccacaggactgaagatcaatgtggataaaacaaagagcttgctggttaacaccacttag]
# protein sequence = [MGDIPKEWRTGYIVKVPKKGDLIDCQNWIGIQLLSLPSKVFARVILKTTKATIDATMREEQAGFRTGRSCADQIATLC
# FIIEQSLEWQSPLFVNFVDFKRTFDVVDQVPIWQILRHYDIPRKIVSIIQSLYRDTNCSVIHNANISTSFEINTVVKQGCLLSPLIFSMVIDWVIKTI
# MNQPRAIEWTTMKKLEDLDFADDIVLLSHSHRHMQDKTENLTNVAKTTGLKINVDKTKSLLVNTT]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MZ4.prfl --predictionStart=70557  --predictionEnd=113478  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig620180911_busco_2432604931_.temp