# 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..422]--> unknown_A (34) <--[0..1]--> unknown_B (66) <--[1..7]--> unknown_C (42) <--[0..4]--> unknown_D (47) <--[0..0]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig11178220180911_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 = 1675, name = Contig111782) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig111782	AUGUSTUS	gene	1	738	0.98	+	.	g1
Contig111782	AUGUSTUS	transcript	1	738	0.98	+	.	g1.t1
Contig111782	AUGUSTUS	intron	1	549	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig111782	AUGUSTUS	CDS	550	738	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig111782	AUGUSTUS	stop_codon	736	738	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tccattttggaatataatggtgcggccatcatcgccatgaaaggccgggattgcgtggccatcgcctcggaccgaaggt
# ttggaatacaagctcagacggtcagcacgaacttccagaaaatctttgagatgggaccgagattgtacatcggcttgcctggtctaggcacagatgtc
# caaacagtgtag]
# protein sequence = [SILEYNGAAIIAMKGRDCVAIASDRRFGIQAQTVSTNFQKIFEMGPRLYIGLPGLGTDVQTV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370R3M.prfl --predictionStart=0  --predictionEnd=21611  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig11178220180911_busco_2432604931_.temp