# 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
# --[10..126]--> unknown_B (24) <--[1..12]--> unknown_C (34) <--[2..7]--> unknown_D (21) <--[3..13]--> unknown_E (24) <--[3..30]--> unknown_F (15) <--[1..9]--> unknown_G (19) <--[3..40]--> unknown_H (13) <--[1..29]--> unknown_I (15) <--[7..43]--> unknown_J (23) <--[0..39]--> unknown_K (12) <--[0..2]--> unknown_L (41) <--[1..11]--> unknown_M (29) <--[1..22]--> unknown_N (10) <--[1..18]--> unknown_O (11) <--[0..36]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1759820180911_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 = 20958, name = Contig17598) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig17598	AUGUSTUS	gene	12096	19546	0.13	+	.	g1
Contig17598	AUGUSTUS	transcript	12096	19546	0.13	+	.	g1.t1
Contig17598	AUGUSTUS	tss	12096	12096	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	12096	12239	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	12348	12597	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	start_codon	12543	12545	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	12598	12681	0.59	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	12803	16739	0.62	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	16815	17068	0.67	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	17081	17144	0.64	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	17189	18905	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	intron	19076	19394	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	12543	12597	0.62	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	12682	12802	0.61	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	12682	12802	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	16740	16814	0.7	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	16740	16814	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	17069	17080	0.66	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	17069	17080	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	17145	17188	0.51	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	17145	17188	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	18906	19075	0.63	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	18906	19075	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	CDS	19395	19475	0.64	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	exon	19395	19546	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	stop_codon	19473	19475	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17598	AUGUSTUS	tts	19546	19546	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttcacaaagattttgatagttcttgagtacaaggctggatttgtttacaaagatgatgatactccagactgtcagt
# atgtagacctgctgttgaatcctgagaggtacactggttataagggcgcttcccctcacaggatttggaacagtatttatgaggaaaactgcttcaag
# gctaaggtcaagcctgaacagaagctttacataggaacaataggatttaacttctcgtcacccagcatcttcagggtctttggaagctcaaatgcatg
# cagtatttacgtgatgcaccatgtgattgattccaccaccctgctgtcttcaccggagttccggccgaacaccgaggaattcatcatgcgatttgatc
# ctaaagctaccaaaggccaggggccacaacgattgaaaaacctttactttacttacctggtagagttacgggccctggctaaggctgcaccttatcta
# gagaaggaagaatttttcacgggaagtcctgaggaggaaaaagatataaaggagggcatcaaggatctactgaaaatcatcaagtga]
# protein sequence = [MFTKILIVLEYKAGFVYKDDDTPDCQYVDLLLNPERYTGYKGASPHRIWNSIYEENCFKAKVKPEQKLYIGTIGFNFS
# SPSIFRVFGSSNACSIYVMHHVIDSTTLLSSPEFRPNTEEFIMRFDPKATKGQGPQRLKNLYFTYLVELRALAKAAPYLEKEEFFTGSPEEEKDIKEG
# IKDLLKIIK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QMM.prfl --predictionStart=0  --predictionEnd=20958  --species=fly ./tmp/Contig1759820180911_busco_2432604931_.temp