# 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..177]--> unknown_A (54) <--[0..4]--> unknown_B (25) <--[1..2]--> unknown_C (21) <--[0..2]--> unknown_D (13) <--[0..2]--> unknown_E (15) <--[2..70]--> unknown_F (22) <--[0..2]--> unknown_G (16) <--[1..2]--> unknown_H (37) <--[0..16]--> unknown_I (23) <--[1..45]--> unknown_J (32) <--[8..20]--> unknown_L (23) <--[13..46]--> unknown_N (28) <--[7..15]--> unknown_O (39) <--[17..85]--> unknown_Q (22) <--[10..110]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4942920180911_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 = 5444, name = Contig49429) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig49429	AUGUSTUS	gene	4404	4858	0.2	+	.	g1
Contig49429	AUGUSTUS	transcript	4404	4858	0.2	+	.	g1.t1
Contig49429	AUGUSTUS	start_codon	4404	4406	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	intron	4472	4559	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	intron	4696	4774	0.22	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	CDS	4404	4471	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	CDS	4560	4695	0.76	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	CDS	4775	4858	0.22	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49429	AUGUSTUS	stop_codon	4856	4858	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagctgtaccatgcactgccattcttctgttatcttctggggtggtgccttcagaaatgggcaaggttaccacagt
# tgtttaatatagctgcagcagtggtgtcaacattcatggtgtgctggttgccctttataagatcgaaggagagtgtctcacaagttcttcacagggtg
# ttccctttggcaagaggactgtatgagttattgttcttctgtgaatgcagaattctagatgattgtttcaggataaagttgcgaatgtgtggtgcagt
# ttgtcagtcctaa]
# protein sequence = [MELYHALPFFCYLLGWCLQKWARLPQLFNIAAAVVSTFMVCWLPFIRSKESVSQVLHRVFPLARGLYELLFFCECRIL
# DDCFRIKLRMCGAVCQS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FSS.prfl --predictionStart=0  --predictionEnd=24875  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4942920180911_busco_2432604931_.temp