# 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..30]--> unknown_A (11) <--[1..4]--> unknown_B (9) <--[1..13]--> unknown_C (33) <--[0..2]--> unknown_D (71) <--[8..17]--> unknown_E (38) <--[6..8]--> unknown_F (20) <--[1..36]--> unknown_G (9) <--[28..121]--> unknown_H (13) <--[0..84]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig17319020180911_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 = 6110, name = Contig173190) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig173190	AUGUSTUS	gene	1	1440	0.54	+	.	g1
Contig173190	AUGUSTUS	transcript	1	1440	0.54	+	.	g1.t1
Contig173190	AUGUSTUS	intron	1	966	0.76	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig173190	AUGUSTUS	CDS	967	1440	0.56	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig173190	AUGUSTUS	stop_codon	1438	1440	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gccccggaccatcgggccatcgattattttgagccctggcggaaaccacacatcttcacatacaccattcatggagttc
# ccctagcctcagtgaagacagcaaaattcttgggagttaacatcattatcaatctcacctggacaccccacactgacaacgttgtaaagaaggcaaac
# aacaccactgcctttctccgccataacatcatcacttgcacaagcaagatcaaggagaagtgctacaggaccatagtatgcagaccagttatagaata
# tgcatgtatagtttgggatcctatcatgcagagggacaccaacaagatagaaatggtccaaaggagagctgcatgttttgtctatggagactacatga
# caacacgcagtgttacatctaaaaactccagtgggacacactacaacacagaagacaagaccttaaggtcactgtgctattcagaatcatcaatggac
# tag]
# protein sequence = [APDHRAIDYFEPWRKPHIFTYTIHGVPLASVKTAKFLGVNIIINLTWTPHTDNVVKKANNTTAFLRHNIITCTSKIKE
# KCYRTIVCRPVIEYACIVWDPIMQRDTNKIEMVQRRAACFVYGDYMTTRSVTSKNSSGTHYNTEDKTLRSLCYSESSMD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SON.prfl --predictionStart=0  --predictionEnd=22191  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig17319020180911_busco_2432604931_.temp