# 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..110]--> unknown_A (7) <--[0..3]--> unknown_B (15) <--[3..23]--> unknown_C (52) <--[7..71]--> unknown_D (21) <--[6..12]--> unknown_F (20) <--[4..9]--> unknown_G (34) <--[0..104]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5329220180911_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 = 2875, name = Contig53292) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig53292	AUGUSTUS	gene	1	1489	0.55	+	.	g1
Contig53292	AUGUSTUS	transcript	1	1489	0.55	+	.	g1.t1
Contig53292	AUGUSTUS	intron	1	361	0.71	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53292	AUGUSTUS	intron	482	1330	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53292	AUGUSTUS	CDS	362	481	0.63	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53292	AUGUSTUS	CDS	1331	1489	0.91	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53292	AUGUSTUS	stop_codon	1487	1489	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tgtttaagcagtggtcacccatcagtgtgtaaccagtatcaagttacctttaatcacacatccatgtgtaagcaggaca
# aagttgcctcgggtcatccatcagtgtgtaggcaatacaaaggagacatcggcccgttcacacctggtttacctgtgcaggtgccgctatggatggct
# gtaaatctcaaacaaggacagaagtgtagagttctaccaccggaatggatggatattggtcagtatatataccatctcgagaagagctttatcatcac
# ttga]
# protein sequence = [CLSSGHPSVCNQYQVTFNHTSMCKQDKVASGHPSVCRQYKGDIGPFTPGLPVQVPLWMAVNLKQGQKCRVLPPEWMDI
# GQYIYHLEKSFIIT]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SC9.prfl --predictionStart=0  --predictionEnd=21522  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5329220180911_busco_2432604931_.temp