# 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
# --[3..588]--> unknown_A (6) <--[1..4]--> unknown_B (8) <--[2..4]--> unknown_C (76) <--[0..11]--> unknown_D (8) <--[0..1]--> unknown_E (61) <--[0..2]--> unknown_F (15) <--[1..2]--> unknown_G (39) <--[5..64]--> unknown_H (13) <--[0..18]--> unknown_I (30) <--[6..11]--> unknown_J (15) <--[0..213]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8651720180911_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 = 1617, name = Contig86517) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig86517	AUGUSTUS	gene	14	1008	0.83	-	.	g1
Contig86517	AUGUSTUS	transcript	14	1008	0.83	-	.	g1.t1
Contig86517	AUGUSTUS	stop_codon	14	16	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86517	AUGUSTUS	intron	220	968	0.86	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86517	AUGUSTUS	CDS	14	219	0.96	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86517	AUGUSTUS	CDS	969	1008	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86517	AUGUSTUS	start_codon	1006	1008	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagactctacgagatttaccagatgcacgtgtgctccggtaaacagaagagtaagaaggcagtaaatccagaggaat
# tactggaagttccgaagggctggaaggagccgggaatctcaaaggaacagaaccctcatggcatggtcagcgaaagctcgtttgccacgctgttcccg
# aaataccgggaaacttacatcaccgactgctggccgctcgtaaagaaaacactggcagatcatgtatga]
# protein sequence = [MRLYEIYQMHVCSGKQKSKKAVNPEELLEVPKGWKEPGISKEQNPHGMVSESSFATLFPKYRETYITDCWPLVKKTLA
# DHV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KD4.prfl --predictionStart=0  --predictionEnd=20118  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8651720180911_busco_2432604931_.temp