# 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..82]--> unknown_A (8) <--[0..2]--> unknown_B (15) <--[0..1]--> unknown_C (8) <--[0..12]--> unknown_D (60) <--[13..36]--> unknown_F (16) <--[0..5]--> unknown_G (17) <--[0..12]--> unknown_H (15) <--[1..32]--> unknown_I (30) <--[0..18]--> unknown_J (21) <--[0..302]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2344320180911_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 = 19713, name = Contig23443) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig23443	AUGUSTUS	gene	758	4345	0.11	+	.	g1
Contig23443	AUGUSTUS	transcript	758	4345	0.11	+	.	g1.t1
Contig23443	AUGUSTUS	start_codon	758	760	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	intron	853	2386	0.29	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	intron	2469	4198	0.56	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	CDS	758	852	0.3	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	CDS	2387	2468	0.82	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	CDS	4199	4345	0.35	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig23443	AUGUSTUS	stop_codon	4343	4345	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggtccgcccgcgatgtaattctaatggtcgcccccgcgatgtaattcttatatggtcgccccgcgatgtaattctgt
# atggtcgccccgcgatattcgccagggaatacactcggagtgtaccattcaatatggacaagattaaaatcaccacctatatcaagccagaagacctg
# caacggcacacgccgttcccgacgacatccaccgtcgtccccgacgaaatcacgtccgtacaccagagctccggagagactctacccgacacaggtct
# accgccaaacaccagagtcactacgctgccaccaaattgtaacgtgtag]
# protein sequence = [MVRPRCNSNGRPRDVILIWSPRDVILYGRPAIFAREYTRSVPFNMDKIKITTYIKPEDLQRHTPFPTTSTVVPDEITS
# VHQSSGETLPDTGLPPNTRVTTLPPNCNV]
# end gene g1
###
# start gene g2
Contig23443	AUGUSTUS	gene	5002	8554	0.13	-	.	g2
Contig23443	AUGUSTUS	transcript	5002	8554	0.13	-	.	g2.t1
Contig23443	AUGUSTUS	stop_codon	5002	5004	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	intron	5168	5848	0.35	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	intron	5940	8481	0.32	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	CDS	5002	5167	0.35	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	CDS	5849	5939	0.35	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	CDS	8482	8554	0.33	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig23443	AUGUSTUS	start_codon	8552	8554	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgacacggtcgcaccccaagaaaaaattaaagaactattcatttgcatgtcacaaccgagagggaggcaaaggtacaa
# ttatcttgggtgaaattcttcctccagcagtgataacagaagtcagcggaaatggatttccagcacagagctggaggaaagacagcaacggcacacgc
# cgttcccgacgacatccaccgtcgtccccggacgaaatcacgtccgtacaccagagctccggagagactctacccgacacaggtctaccgccaaacac
# cagagtcactaccaccaaaattgtaacgtgtagcggtcacccatccagatgctga]
# protein sequence = [MTRSHPKKKLKNYSFACHNREGGKGTIILGEILPPAVITEVSGNGFPAQSWRKDSNGTRRSRRHPPSSPDEITSVHQS
# SGETLPDTGLPPNTRVTTTKIVTCSGHPSRC]
# end gene g2
###
# start gene g3
Contig23443	AUGUSTUS	gene	8723	13812	0.13	-	.	g3
Contig23443	AUGUSTUS	transcript	8723	13812	0.13	-	.	g3.t1
Contig23443	AUGUSTUS	stop_codon	8723	8725	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	intron	8882	9895	0.51	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	intron	9968	10894	0.51	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	intron	11059	11984	0.84	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	intron	12129	13538	0.45	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	CDS	8723	8881	0.29	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	CDS	9896	9967	0.57	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	CDS	10895	11058	0.75	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	CDS	11985	12128	0.67	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	CDS	13539	13812	0.43	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23443	AUGUSTUS	start_codon	13810	13812	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgcccctggtggcatacccgggggaggaacgggtgtatggtacagggggcggggagggggcttggcatgttgggaggg
# gcccgggagggggcatgcctgcaggtggaatatgggggggagggcatcccgggcccactggtggtcgccagcgacgaggtgcggcattggggcctcct
# cgcttgtgccatgggggtggggggaggcatcctggaggggtggggcatgcgagggagggggaggaagctgtgtgcttctatggggctggagccgcagt
# gtttaatgaattttatatattatatgttgccagggctcgtcgagcagccaaggaagccaaagaagccccagcccaaccagcccctgagaaagcccggg
# tggatatcaagaaattcgtcaaaattggaaggcccggttacaaagactctctattgtgcattatccagattgactaccccgagattgtggaaggcatt
# gctccacgtcacagatttatggcagcttatgaacaaaaggtggagcctccagacagaaaatggcaatatctcttgtttgctgccgaaccttacgaaac
# aatagcattcaaggatccttattttatgaagaatcacttggggtcatatgaatgtaaactatgtctgactcttcacaacaatgagcaacggcacccgc
# cgttcctgacgacatccaacgtcgtctccggacgaaaccacgtccgtacccagagctccgaagagactctacctgacacccgacctgacacaggtttc
# ctgccaaacattagagtcactacgctgccaccaatttgtaacgtgtag]
# protein sequence = [MPLVAYPGEERVYGTGGGEGAWHVGRGPGGGMPAGGIWGGGHPGPTGGRQRRGAALGPPRLCHGGGGRHPGGVGHARE
# GEEAVCFYGAGAAVFNEFYILYVARARRAAKEAKEAPAQPAPEKARVDIKKFVKIGRPGYKDSLLCIIQIDYPEIVEGIAPRHRFMAAYEQKVEPPDR
# KWQYLLFAAEPYETIAFKDPYFMKNHLGSYECKLCLTLHNNEQRHPPFLTTSNVVSGRNHVRTQSSEETLPDTRPDTGFLPNIRVTTLPPICNV]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QJ1.prfl --predictionStart=0  --predictionEnd=31044  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2344320180911_busco_2432604931_.temp