# 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
# --[10..202]--> unknown_B (26) <--[0..15]--> unknown_C (10) <--[0..2]--> unknown_D (41) <--[0..29]--> unknown_E (91) <--[0..0]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8553820180911_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 = 10410, name = Contig85538) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig85538	AUGUSTUS	gene	4979	10410	0.2	-	.	g1
Contig85538	AUGUSTUS	transcript	4979	10410	0.2	-	.	g1.t1
Contig85538	AUGUSTUS	stop_codon	4979	4981	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	intron	5111	7194	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	intron	7324	8252	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	intron	8426	8483	0.9	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	intron	8499	9478	0.78	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	intron	9556	10410	0.28	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	CDS	4979	5110	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	CDS	7195	7323	0.87	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	CDS	8253	8425	0.96	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	CDS	8484	8498	0.85	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig85538	AUGUSTUS	CDS	9479	9555	0.36	-	1	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aaaagaaccagaggtgacaatagaagctatgacaaacagatttgtgatgtattcctttgctcaggaagttgttgcagtg
# ccagagctaaccagtatgagaactgtgctgggaatgctttttaaggagccagccacactgaactatccgtttgagaaaggtccgctgagtccccgatt
# tcgaggagagcatgcgctgaggaggtacccctcaggcgaggagagatgcattgcttgtaaactctgtgaggccatctgtccggcacaggccatcacta
# ttgaagccgagacgcgggctgacggaagcagaaggactacgcgatacgatatcgacatgacaaaatgtatttactgcggattctgtcaggaggcgtgt
# ccagtggatgccattgtggagggccctaactttgaatactctacggagactcacgaagaacttctgtacaacaaagaaaagctactgagtaatgggga
# caaatgggaggtagagatagcagctaacctgcaggctgaccacatgtacagataa]
# protein sequence = [KEPEVTIEAMTNRFVMYSFAQEVVAVPELTSMRTVLGMLFKEPATLNYPFEKGPLSPRFRGEHALRRYPSGEERCIAC
# KLCEAICPAQAITIEAETRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYNKEKLLSNGDKWEVEIAANLQADHMYR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RIT.prfl --predictionStart=0  --predictionEnd=28414  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8553820180911_busco_2432604931_.temp