# 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..96]--> unknown_A (20) <--[1..17]--> unknown_B (16) <--[0..30]--> unknown_C (18) <--[0..33]--> unknown_D (20) <--[1..11]--> unknown_E (11) <--[0..1]--> unknown_F (12) <--[3..25]--> unknown_G (20) <--[8..194]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5254320180911_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 = 6729, name = Contig52543) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig52543	AUGUSTUS	gene	1	6385	0.52	+	.	g1
Contig52543	AUGUSTUS	transcript	1	6385	0.52	+	.	g1.t1
Contig52543	AUGUSTUS	intron	1	554	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	intron	649	2078	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	intron	2254	3949	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	intron	4091	4508	0.9	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	intron	4585	5417	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	intron	5553	6188	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	555	648	0.68	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	2079	2253	0.76	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	3950	4090	0.91	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	4509	4584	0.95	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	5418	5552	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	CDS	6189	6385	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig52543	AUGUSTUS	stop_codon	6383	6385	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gttatgtgactgatgtcctggaagatgctaaagtctactctaaccatgccaacaagaaagcgctggacgctgaggacat
# caaactggctgtgcatcctactctagagccactcaacagaaagcggctggatgcggagggacataatctggcttgtgcagtggtcgtatggcaatcgt
# acacaagtccactccagagatgtaaggaattgacactatattttatcagtctcggtgcatcggaggtttttatcactggcgaacacttacatcttctg
# atggagatctccaagcacaagaacagccaggttcttcctctgattaagccgtacacggggctgcgactgcccccggacaggtactgtttgtctgcccc
# gaactacaaaatgaccagtcacaaggcagtcaaaaagcatcaggctaggatacagattggaataccacagttccagcagagaatcaacctgagtcaga
# tgtccatgacacctggtaagcttagtgctggaggtccacaccttacagtggtcactaaaccaggcatgactgttcctgctgttaccatagtaaccaag
# ccatctggccatcacccaacaatgaccaaaccagccatacgaatctccacgggcccatcgttgaactccttaaaccaggtccgtgcattccagcacag
# catgccgggggccagcagctatcagtctgcccctcagtcaaccatacagttccagcccttacagagcaccacaacatcactcatcaccggccaaccat
# taaatccactcaagcggaaaatgcaagaggatgactatgataatccatcctga]
# protein sequence = [YVTDVLEDAKVYSNHANKKALDAEDIKLAVHPTLEPLNRKRLDAEGHNLACAVVVWQSYTSPLQRCKELTLYFISLGA
# SEVFITGEHLHLLMEISKHKNSQVLPLIKPYTGLRLPPDRYCLSAPNYKMTSHKAVKKHQARIQIGIPQFQQRINLSQMSMTPGKLSAGGPHLTVVTK
# PGMTVPAVTIVTKPSGHHPTMTKPAIRISTGPSLNSLNQVRAFQHSMPGASSYQSAPQSTIQFQPLQSTTTSLITGQPLNPLKRKMQEDDYDNPS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937186Q.prfl --predictionStart=0  --predictionEnd=24066  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5254320180911_busco_2432604931_.temp