# 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..246]--> unknown_A (24) <--[13..80]--> unknown_C (12) <--[0..61]--> unknown_D (27) <--[1..4]--> unknown_E (24) <--[0..1]--> unknown_F (72) <--[0..1]--> unknown_G (47) <--[0..1]--> unknown_H (14) <--[0..66]--> unknown_I (28) <--[0..1]--> unknown_J (71) <--[0..2]--> unknown_K (10) <--[0..2]--> unknown_L (27) <--[0..8]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8570820180911_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 = 9879, name = Contig85708) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig85708	AUGUSTUS	gene	4885	9668	0.02	-	.	g1
Contig85708	AUGUSTUS	transcript	4885	9668	0.02	-	.	g1.t1
Contig85708	AUGUSTUS	stop_codon	4885	4887	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	4971	7030	0.43	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	7071	7334	0.57	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	7389	7458	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	7656	8022	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	8132	8610	0.5	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	intron	8831	9594	0.34	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	4885	4970	0.49	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	7031	7070	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	7335	7388	0.75	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	7459	7655	0.47	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	8023	8131	0.65	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	8611	8830	0.64	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	CDS	9595	9668	0.48	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85708	AUGUSTUS	start_codon	9666	9668	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggcagtcatacttttttttttcttgctgttgacaattttgaagaatacttggagatctattctcgtcttgtcctga
# ttgatgaaggtggcgactgggaccgtaggaaccgactgaaggtgtaccgtggaatctactgtatgtcaatacgcgactttaaacaggcggcagcacta
# tttctggataccgtggcaacattcacatcctacgagttaatggactaccagtcgtttgtcacctacaccgtgctgtgtagtatgatcgcaatggagag
# gccagatctcagggaaaaggttgtgaaggggtctgaaattcttgaagtcctgcacagtctcccaaaagtccgttcctttctgtttgctcttcatgact
# gccattactcagatttcttcagatatttagctcaggtggaggacacttttgattatttgttgtttgggcctacagctcaggtcgaggacactttgatt
# attgttgtttggcctacagctcaggtcgaggacacttatgatttttgttgtttgacctacagctcaggtagaggacactttgattatttgttgtttga
# cctacagctcagtgtcgaggacacgttgaagctactggagtcctacagaagtctcactctggactacatggccaacgctttcgggatgagatggagac
# ctaaaatagccaaaatgctacttaaaggctacaataaaacagggagatatcttgttgaacagagtccaaaagctgagccgggtgatcaacatatgaat
# ctgatctataaatag]
# protein sequence = [MGSHTFFFLAVDNFEEYLEIYSRLVLIDEGGDWDRRNRLKVYRGIYCMSIRDFKQAAALFLDTVATFTSYELMDYQSF
# VTYTVLCSMIAMERPDLREKVVKGSEILEVLHSLPKVRSFLFALHDCHYSDFFRYLAQVEDTFDYLLFGPTAQVEDTLIIVVWPTAQVEDTYDFCCLT
# YSSGRGHFDYLLFDLQLSVEDTLKLLESYRSLTLDYMANAFGMRWRPKIAKMLLKGYNKTGRYLVEQSPKAEPGDQHMNLIYK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FLD.prfl --predictionStart=0  --predictionEnd=28832  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8570820180911_busco_2432604931_.temp