# 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
# --[7..177]--> unknown_A (112) <--[1..39]--> unknown_B (128) <--[0..3]--> unknown_C (27) <--[2..7]--> unknown_D (146) <--[7..15]--> unknown_E (51) <--[1..4]--> unknown_F (68) <--[0..1]--> unknown_G (8) <--[4..11]--> unknown_H (27) <--[0..3]--> unknown_I (13) <--[4..641]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6230820180911_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 = 11618, name = Contig62308) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig62308	AUGUSTUS	gene	1	9269	0.04	+	.	g1
Contig62308	AUGUSTUS	transcript	1	9269	0.04	+	.	g1.t1
Contig62308	AUGUSTUS	intron	1	216	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	intron	380	1057	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	intron	1223	7714	0.14	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	intron	7874	9074	0.34	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	CDS	217	379	0.85	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	CDS	1058	1222	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	CDS	7715	7873	0.19	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	CDS	9075	9269	0.33	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62308	AUGUSTUS	stop_codon	9267	9269	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [agaatttacaatggccgaaattgagcacttctgtgacccagtgaagaaggatcatccaaagttccagtcagtagcggat
# ctagaggtggtgttgtattcagcctgtaatcaaatggacgggaaatcccctcaagtgtggaagctcggggaggctgtcaaacagaaattaatagccaa
# tgagacgcttggatattttatggggaggatccagttatttatgattaagtgtggcattgacaaaaggaagctgagatttcgacaacacatgtccaacg
# agatggcacattatgcttgtgattgctgggatgcggagtgcaaaactacatacaatattaaacacaaaagtataatccatgctttgaaagatatattt
# gaaggaggcagaattccttttgaactgaggacggataaaggatcagaatggatcaacagatggaccaaacagtatgtgaagaggaaagacttacatca
# ttatgtcacgcaaaataatgtgttcaacaagggaaaagaaaatcgaacaatgaacttaattaaacaatcagtacatatagttctgtttaaaaatccca
# gagatcgacaacagatcggaaccctagcacggcggatgtacccaggaaatgccaagaagcttctagacgcttatgaaaaagcggtatcaattccctac
# ggagcactgtgttag]
# protein sequence = [EFTMAEIEHFCDPVKKDHPKFQSVADLEVVLYSACNQMDGKSPQVWKLGEAVKQKLIANETLGYFMGRIQLFMIKCGI
# DKRKLRFRQHMSNEMAHYACDCWDAECKTTYNIKHKSIIHALKDIFEGGRIPFELRTDKGSEWINRWTKQYVKRKDLHHYVTQNNVFNKGKENRTMNL
# IKQSVHIVLFKNPRDRQQIGTLARRMYPGNAKKLLDAYEKAVSIPYGALC]
# end gene g1
###
# start gene g2
Contig62308	AUGUSTUS	gene	9945	10211	0.16	+	.	g2
Contig62308	AUGUSTUS	transcript	9945	10211	0.16	+	.	g2.t1
Contig62308	AUGUSTUS	start_codon	9945	9947	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig62308	AUGUSTUS	CDS	9945	10211	0.16	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig62308	AUGUSTUS	stop_codon	10209	10211	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgttacccaaggacagaaacttgcttcttaagaagtacaaaagtattcttttactttttgctcagttgaatcaaagca
# aactccaccgcaacatcaagaaagaagtattcaccctcatgaagactaaggacatagatctggaaagggcagtttcccgtgttcttaataaatataga
# catgaatttgagcatctgttggaggccgatggcagcttttaccatgacaataccgcggatttgtctggcgacgagcaaataaatgaataa]
# protein sequence = [MLPKDRNLLLKKYKSILLLFAQLNQSKLHRNIKKEVFTLMKTKDIDLERAVSRVLNKYRHEFEHLLEADGSFYHDNTA
# DLSGDEQINE]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705YA.prfl --predictionStart=0  --predictionEnd=21222  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6230820180911_busco_2432604931_.temp