# 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..891]--> unknown_A (12) <--[9..16]--> unknown_C (22) <--[5..40]--> unknown_D (20) <--[0..2]--> unknown_E (26) <--[0..23]--> unknown_F (22) <--[2..26]--> unknown_G (23) <--[0..11]--> unknown_H (31) <--[3..107]--> unknown_I (15) <--[0..36]--> unknown_J (17) <--[1..2]--> unknown_K (27) <--[0..1]--> unknown_L (12) <--[0..6]--> unknown_M (13) <--[1..54]--> unknown_N (13) <--[0..17]--> unknown_O (10) <--[0..103]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9807020180911_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 = 9779, name = Contig98070) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig98070	AUGUSTUS	gene	302	6122	0.04	-	.	g1
Contig98070	AUGUSTUS	transcript	302	6122	0.04	-	.	g1.t1
Contig98070	AUGUSTUS	stop_codon	302	304	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	intron	341	3553	0.16	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	intron	3672	3837	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	intron	4009	5985	0.4	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	CDS	302	340	0.17	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	CDS	3554	3671	0.96	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	CDS	3838	4008	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	CDS	5986	6122	0.17	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig98070	AUGUSTUS	start_codon	6120	6122	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtatcacaaccaacaacttcagcctgcaactgttaaatcagcatcaatgtatccaccaaccaacaactcaagcctgc
# aaactgttaaaccaagcatcaatgatatcaccaaccaacaaaacttcagcctgcaactgaagaggttaagattatcagagaacaggtcatttggaaat
# gatgtgtacagagtgacgtatgaattagatgaccttgacaacgttcccttgtttggggccaaatataacttccatctagagggtgttgtggattgtcc
# tgaatttttagtatacttcccagtgcttgaaaagttggctgaggaatatggtatgaaacttgtttataagaaatcatttgcagaatactttgcagaaa
# atgtggagaagggggaacacagaaatctactgaataaaatgcaaagcttagaggtcatctcgacatttgatcctgcggactcgtgcttgtag]
# protein sequence = [MYHNQQLQPATVKSASMYPPTNNSSLQTVKPSINDITNQQNFSLQLKRLRLSENRSFGNDVYRVTYELDDLDNVPLFG
# AKYNFHLEGVVDCPEFLVYFPVLEKLAEEYGMKLVYKKSFAEYFAENVEKGEHRNLLNKMQSLEVISTFDPADSCL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370J9L.prfl --predictionStart=0  --predictionEnd=24007  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9807020180911_busco_2432604931_.temp