# 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
# --[20..245]--> unknown_B (16) <--[0..9]--> unknown_C (46) <--[4..6]--> unknown_D (12) <--[0..65]--> unknown_E (34) <--[0..4]--> unknown_F (16) <--[6..35]--> unknown_G (19) <--[0..17]--> unknown_H (9) <--[9..33]--> unknown_I (15) <--[0..4]--> unknown_J (17) <--[1..2]--> unknown_K (45) <--[11..32]--> unknown_M (20) <--[1..6]--> unknown_N (25) <--[0..36]--> unknown_O (18) <--[1..12]--> unknown_P (26) <--[0..24]--> unknown_Q (24) <--[0..37]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6330620180911_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 = 5552, name = Contig63306) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig63306	AUGUSTUS	gene	1	2760	0.35	+	.	g1
Contig63306	AUGUSTUS	transcript	1	2760	0.35	+	.	g1.t1
Contig63306	AUGUSTUS	intron	1	1246	0.43	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63306	AUGUSTUS	intron	1455	2555	0.6	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63306	AUGUSTUS	CDS	1247	1454	0.42	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig63306	AUGUSTUS	CDS	2556	2760	0.76	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig63306	AUGUSTUS	stop_codon	2758	2760	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ttacagggcgtcatcaagaatggcggaagtttggtggaattccatttgcaattaaggacaacttctgtacgaaagatat
# caggacaacatgtgcttctaaaatgctcagtaattttgtacctccatacactgcaactgtagttcaaaggttacaggatgaaggagctgttgttattg
# ccaaaactaatatggatgaatttggtatgggggcctttggttcggatacaggtggttccactaggaaccctgcggcttactgtggagtggttggtttc
# aaggcaacttacggacgcctgtccagacatggcctgattccactagttaactcccttgatgtaccaggaatactggccaaaagtgtggatgatgcaag
# tctcatgnnnnnnnnnnnnnnnnnnnnnnnnnttcagtag]
# protein sequence = [TGRHQEWRKFGGIPFAIKDNFCTKDIRTTCASKMLSNFVPPYTATVVQRLQDEGAVVIAKTNMDEFGMGAFGSDTGGS
# TRNPAAYCGVVGFKATYGRLSRHGLIPLVNSLDVPGILAKSVDDASLMXXXXXXXXXQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OFR.prfl --predictionStart=0  --predictionEnd=22718  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6330620180911_busco_2432604931_.temp