# 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..24]--> unknown_A (7) <--[0..2]--> unknown_B (25) <--[7..34]--> unknown_D (24) <--[0..1]--> unknown_E (7) <--[0..2]--> unknown_F (52) <--[5..15]--> unknown_G (14) <--[0..99]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5987020180911_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 = 30015, name = Contig59870) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig59870	AUGUSTUS	gene	12196	13867	0.16	+	.	g1
Contig59870	AUGUSTUS	transcript	12196	13867	0.16	+	.	g1.t1
Contig59870	AUGUSTUS	start_codon	12196	12198	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	intron	12262	12410	0.35	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	intron	12497	13546	0.23	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	intron	13666	13796	0.74	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	CDS	12196	12261	0.49	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	CDS	12411	12496	0.35	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	CDS	13547	13665	0.75	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	CDS	13797	13867	0.75	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig59870	AUGUSTUS	stop_codon	13865	13867	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaatggcagttggcggcaatggttagtccgaaggtgttgcagtcacacgattcacacattcaggatccaggtcact
# accgccgcaaaaatgcactccttgactccaaagtcaagcaaacaatctttttgtcattgactagtgaaaagatcttacgtcaggaagtgagctttgca
# gcttatcttccagtcctgggagagactctcaaccatgcccgtgtcgtggacttcgttattgctataattgttgatgcacatgccatcactgtaaatac
# tctcaagcatgcccgtgtcgtggacttcgttattgctattgttgatgcacatgccatcactgtgtaa]
# protein sequence = [MEWQLAAMVSPKVLQSHDSHIQDPGHYRRKNALLDSKVKQTIFLSLTSEKILRQEVSFAAYLPVLGETLNHARVVDFV
# IAIIVDAHAITVNTLKHARVVDFVIAIVDAHAITV]
# end gene g1
###
# start gene g2
Contig59870	AUGUSTUS	gene	14771	16355	0.13	-	.	g2
Contig59870	AUGUSTUS	transcript	14771	16355	0.13	-	.	g2.t1
Contig59870	AUGUSTUS	stop_codon	14771	14773	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	intron	15000	15710	0.2	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	intron	15785	16034	0.22	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	CDS	14771	14999	0.63	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	CDS	15711	15784	0.17	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	CDS	16035	16355	0.5	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59870	AUGUSTUS	start_codon	16353	16355	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgcaactggctttccagtctaattctagggtaacttatttactggccagcggtgaccaatggagttgggctgttgtcg
# ccgtcaccattgcgccgtcagcccatctcgcaaaagtccattatatggtcaatctgcgagagacatcttgtaccactcgcattagaaagaacagcttc
# accattctcaagatggaaccacaacaacccattccaagggaatctttccctggaattccgaccaacaataatgcagatgccatggaaaccgaagtcct
# tatggtggaacagctgtatcgtatacggatccatggcccagagggagcccgcgaacagatagccctctttggctgcaagttgagggaggtgcagacca
# ggcacgaccgggcaacggaggtcccgttagaagttcttccgaaagattcgcacgttgccaacatcctgtcaggggaagtggaagatcttccgattcgt
# gtcatggggtttaagaatgacctgaacgaggtcaacattcccacgcgtttcctgttcctgtctgggcagacgtgggaaagagaaggagttggtggaat
# ttggcagatgtatgggaacgatgatggtggacgaggtatgctcttagaaagatga]
# protein sequence = [MQLAFQSNSRVTYLLASGDQWSWAVVAVTIAPSAHLAKVHYMVNLRETSCTTRIRKNSFTILKMEPQQPIPRESFPGI
# PTNNNADAMETEVLMVEQLYRIRIHGPEGAREQIALFGCKLREVQTRHDRATEVPLEVLPKDSHVANILSGEVEDLPIRVMGFKNDLNEVNIPTRFLF
# LSGQTWEREGVGGIWQMYGNDDGGRGMLLER]
# end gene g2
###
# start gene g3
Contig59870	AUGUSTUS	gene	21128	23077	0.3	-	.	g3
Contig59870	AUGUSTUS	transcript	21128	23077	0.3	-	.	g3.t1
Contig59870	AUGUSTUS	stop_codon	21128	21130	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	intron	21306	21429	0.33	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	intron	21569	22932	0.36	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	CDS	21128	21305	0.5	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	CDS	21430	21568	0.34	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	CDS	22933	23077	0.45	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig59870	AUGUSTUS	start_codon	23075	23077	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggggtttatatgtctaaaggtcaatgacctgaacgaggtcaacattcccacgcgcttcctgttcctgtctgatcaga
# cgtgggaaagagaaggaggaattggtggaatttggcagatgtatgggaacgatgatggtggaagagagggatcttttccgatccacatctgctgtgac
# acgggacctctgtttttccggtctcatccgaaggaccgccccattcagtcgcctcttacgacacgcaaggggatgctggggagctattctaacccgga
# aacccacggtttcttccgaaagatgcccaaaggaccgcacattgccaacatcctgccaggggaagtggaagatcttccgtttcgtgtcatggggttta
# agaatgacctgaacgaggtcaccattccaacgcgcttcctgttcctgtctgggagacgcggggaagaggaggagttgatggaatgttaa]
# protein sequence = [MGFICLKVNDLNEVNIPTRFLFLSDQTWEREGGIGGIWQMYGNDDGGREGSFPIHICCDTGPLFFRSHPKDRPIQSPL
# TTRKGMLGSYSNPETHGFFRKMPKGPHIANILPGEVEDLPFRVMGFKNDLNEVTIPTRFLFLSGRRGEEEELMEC]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370WT1.prfl --predictionStart=0  --predictionEnd=30015  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5987020180911_busco_2432604931_.temp