# 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..663]--> unknown_A (19) <--[1..46]--> unknown_B (38) <--[1..9]--> unknown_C (15) <--[0..24]--> unknown_D (11) <--[0..6]--> unknown_E (11) <--[10..17]--> unknown_F (19) <--[8..19]--> unknown_H (20) <--[1..3]--> unknown_I (18) <--[0..1]--> unknown_J (37) <--[15..40]--> unknown_M (13) <--[1..30]--> unknown_N (20) <--[10..39]--> unknown_O (27) <--[2..8]--> unknown_P (11) <--[8..32]--> unknown_Q (37) <--[11..39]--> unknown_S (20) <--[0..2]--> unknown_T (17) <--[0..32]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig13226920180911_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 = 7232, name = Contig132269) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig132269	AUGUSTUS	gene	3464	7232	0.25	-	.	g1
Contig132269	AUGUSTUS	transcript	3464	7232	0.25	-	.	g1.t1
Contig132269	AUGUSTUS	stop_codon	3464	3466	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	intron	3645	4120	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	intron	4244	5435	0.53	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	intron	5513	7232	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	CDS	3464	3644	0.75	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	CDS	4121	4243	0.5	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig132269	AUGUSTUS	CDS	5436	5512	0.71	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ctcgatgtggatttggatgtggagaatgtggtcatcttgggccagggcaatgtagcactagacgtggccaggattttaa
# ggggccccctacaagtggccttcacgatcaaagagctgcgggagatgacgcggctaccgggttgtagagccgtcatacacaaggatgacgttcataat
# ctcgaccagcttataaaaggcacatctcccacgtcccagaaagaggctaacggaactcctgtttcacatccttgttacagaaacagcatttggagccg
# ctttaatgcggaaggaccccaggcagccacaagaagtgggagcttagatttagactcagtcccacagcgggtgatttctcgcactcgaaccatgagtg
# caggatag]
# protein sequence = [LDVDLDVENVVILGQGNVALDVARILRGPLQVAFTIKELREMTRLPGCRAVIHKDDVHNLDQLIKGTSPTSQKEANGT
# PVSHPCYRNSIWSRFNAEGPQAATRSGSLDLDSVPQRVISRTRTMSAG]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DP4.prfl --predictionStart=0  --predictionEnd=24329  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig13226920180911_busco_2432604931_.temp