# 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..2]--> unknown_A (22) <--[7..16]--> unknown_B (33) <--[0..1]--> unknown_C (7) <--[0..1]--> unknown_D (45) <--[9..36]--> unknown_E (43) <--[16..263]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5641620180911_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 = 5298, name = Contig56416) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig56416	AUGUSTUS	gene	1353	3893	0.08	-	.	g1
Contig56416	AUGUSTUS	transcript	1353	3893	0.08	-	.	g1.t1
Contig56416	AUGUSTUS	stop_codon	1353	1355	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	intron	1420	1508	0.19	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	intron	1670	3887	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	CDS	1353	1419	0.18	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	CDS	1509	1669	0.39	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	CDS	3888	3893	0.52	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56416	AUGUSTUS	start_codon	3891	3893	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcaaaccgacctgaagaacacagactatacactggaggctggtgccacgcgtctttttgaggcggagaaattagtgc
# gacaaatggctgaaaaagaaatcaaagagaaagaagaggaagaactcaacaacccaatggaggtcagtctgatattacagctacatattgtcctacat
# cactcgcttatgatcgcctactacatcacactacagatgtctacatccactgcttaa]
# protein sequence = [MQTDLKNTDYTLEAGATRLFEAEKLVRQMAEKEIKEKEEEELNNPMEVSLILQLHIVLHHSLMIAYYITLQMSTSTA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RCQ.prfl --predictionStart=0  --predictionEnd=22280  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5641620180911_busco_2432604931_.temp