# 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..137]--> unknown_A (13) <--[0..3]--> unknown_B (9) <--[0..2]--> unknown_C (6) <--[0..6]--> unknown_D (11) <--[0..2]--> unknown_E (58) <--[6..7]--> unknown_F (74) <--[1..17]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8607020180911_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 = 17474, name = Contig86070) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig86070	AUGUSTUS	gene	5677	9503	0.18	-	.	g1
Contig86070	AUGUSTUS	transcript	5677	9503	0.18	-	.	g1.t1
Contig86070	AUGUSTUS	stop_codon	5677	5679	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	5799	5949	0.59	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	6038	6085	0.44	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	6163	6395	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	6406	8259	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	8344	8628	0.9	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	intron	8779	9326	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	5677	5798	0.51	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	5950	6037	0.59	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	6086	6162	0.44	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	6396	6405	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	8260	8343	0.88	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	8629	8778	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	CDS	9327	9503	0.66	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86070	AUGUSTUS	start_codon	9501	9503	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcaacacagacagatgacggaatgaatcaaaatgcgagtgaagcagaatttaaagtggtcagatcaaggaaaagga
# aactgaaaccagaaacagagacttcagagtcgggaatggacacatctgccccacctaagaaaccccattttccgccaataagtggtgacaaattgaca
# ggaggaaagtctgaattcagaaaaataccagtaccaagtcacagatacacacctttgaaagaaaactggatgaaaatatttacaccagttgtggaaaa
# actccatcttcagatcagatttaacctcaaaactcgtaatgttgagatcaaaacctgtaaagatacaaaagacatcggatcattacagaaagcagctg
# actttgtgagggccttcacgctaggatttgacattgatctccaggcagtggatgggcagatgtgtctgaattctgtagcatgcattgaatgggatttg
# atgtctccaaatgtatacatgagatgggattccttagctttggttcgactggatgatctctttttggaatcttttgatgtaactgatggcaagtattc
# tattgttatttatttagtaaaacctctgaaaggtgatcatttatcaagagctattggaagagtagcgggtaaaaatggaaggacaaaatttacgatag
# aaaatgttacgaaaaccaggatcgtgttagcagattcgtaa]
# protein sequence = [MATQTDDGMNQNASEAEFKVVRSRKRKLKPETETSESGMDTSAPPKKPHFPPISGDKLTGGKSEFRKIPVPSHRYTPL
# KENWMKIFTPVVEKLHLQIRFNLKTRNVEIKTCKDTKDIGSLQKAADFVRAFTLGFDIDLQAVDGQMCLNSVACIEWDLMSPNVYMRWDSLALVRLDD
# LFLESFDVTDGKYSIVIYLVKPLKGDHLSRAIGRVAGKNGRTKFTIENVTKTRIVLADS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370T9R.prfl --predictionStart=0  --predictionEnd=28766  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8607020180911_busco_2432604931_.temp