# 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..197]--> unknown_A (31) <--[2..18]--> unknown_B (17) <--[2..33]--> unknown_C (17) <--[2..23]--> unknown_D (42) <--[5..19]--> unknown_E (12) <--[1..6]--> unknown_F (15) <--[2..4]--> unknown_G (9) <--[0..1]--> unknown_H (30) <--[3..21]--> unknown_I (28) <--[0..3]--> unknown_J (22) <--[2..19]--> unknown_K (17) <--[0..70]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig13566020180911_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 = 5900, name = Contig135660) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig135660	AUGUSTUS	gene	4456	5900	0.56	-	.	g1
Contig135660	AUGUSTUS	transcript	4456	5900	0.56	-	.	g1.t1
Contig135660	AUGUSTUS	stop_codon	4456	4458	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig135660	AUGUSTUS	intron	4729	5900	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig135660	AUGUSTUS	CDS	4456	4728	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ggtgctatcatggagaagtttggagttcctgcagacaaactgcggatatatcttcattatcagccgtcttactatcatc
# tgcatgttcattttacccacatcatgctgaacagtccgggatttgaagcggatcgagcacatctattgacagatgttgtagaaaatattgagatgaaa
# ccgctctactacaaagaaaaaactctcgcattcaaagtcagagatgatgatgatttatataaagctttcattaatcatggatgtattaagaaataa]
# protein sequence = [GAIMEKFGVPADKLRIYLHYQPSYYHLHVHFTHIMLNSPGFEADRAHLLTDVVENIEMKPLYYKEKTLAFKVRDDDDL
# YKAFINHGCIKK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DX4.prfl --predictionStart=0  --predictionEnd=24725  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig13566020180911_busco_2432604931_.temp