# 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..35]--> unknown_A (50) <--[0..32]--> unknown_B (21) <--[0..2]--> unknown_C (40) <--[1..4]--> unknown_D (28) <--[1..23]--> unknown_E (14) <--[0..6]--> unknown_F (10) <--[1..3]--> unknown_G (15) <--[8..34]--> unknown_I (11) <--[0..2]--> unknown_J (21) <--[10..217]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig19265020180911_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 = 2829, name = Contig192650) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig192650	AUGUSTUS	gene	1	2320	0.09	+	.	g1
Contig192650	AUGUSTUS	transcript	1	2320	0.09	+	.	g1.t1
Contig192650	AUGUSTUS	intron	1	147	0.38	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	intron	233	484	0.6	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	intron	600	1626	0.64	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	intron	1714	1969	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	intron	2039	2284	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	CDS	148	232	0.32	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	CDS	485	599	0.72	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	CDS	1627	1713	0.62	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	CDS	1970	2038	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	CDS	2285	2320	0.36	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig192650	AUGUSTUS	stop_codon	2318	2320	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ctcaacaagatgctgtcaatcttgtatgccattccaaaactcgttccaacccagaaaacaatgtggggctcatatcaat
# gggaagctctgtggatgtcttagtgaccttgacaacagatgtggggcgtcttcttagcaaactacatcaagtacagcccaaaggcatcatcaacttta
# acacggccgtcaaagttgcacatctggcactgaagcatcgacaggggaggaaccacaagatgagaatcgtcgtgtttgtcggaagtcctatagaggac
# gacgagaaagagatggtcaaacttgcaaagaaactgaagaaagaaaaagtcaacattgatatagtcaactttggtgaagagctcagagcatcatgtat
# ggatggtcgaaaaccctaa]
# protein sequence = [QQDAVNLVCHSKTRSNPENNVGLISMGSSVDVLVTLTTDVGRLLSKLHQVQPKGIINFNTAVKVAHLALKHRQGRNHK
# MRIVVFVGSPIEDDEKEMVKLAKKLKKEKVNIDIVNFGEELRASCMDGRKP]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370U0A.prfl --predictionStart=0  --predictionEnd=21707  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig19265020180911_busco_2432604931_.temp