# 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..160]--> unknown_A (6) <--[12..46]--> unknown_B (39) <--[0..1]--> unknown_C (42) <--[1..2]--> unknown_D (14) <--[5..76]--> unknown_E (10) <--[2..53]--> unknown_F (28) <--[1..3]--> unknown_G (8) <--[3..6]--> unknown_H (8) <--[2..20]--> unknown_I (17) <--[3..5]--> unknown_J (7) <--[1..1]--> unknown_K (35) <--[0..53]--> unknown_L (32) <--[0..8]--> unknown_M (18) <--[2..8]--> unknown_N (114) <--[1..24]--> unknown_O (14) <--[0..25]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7273320180911_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 = 8966, name = Contig72733) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig72733	AUGUSTUS	gene	1688	8966	0.14	-	.	g1
Contig72733	AUGUSTUS	transcript	1688	8966	0.14	-	.	g1.t1
Contig72733	AUGUSTUS	stop_codon	1688	1690	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	intron	1856	3533	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	intron	3670	4130	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	intron	4228	8421	0.59	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	intron	8490	8966	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	CDS	1688	1855	0.28	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	CDS	3534	3669	0.81	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	CDS	4131	4227	0.96	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig72733	AUGUSTUS	CDS	8422	8489	0.62	-	1	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tctgtacacctttgacatgcgaaagttgtctgccccagtcatgatgcacatggatcatgtagcagctgtgatggatgtg
# gattattctcctacaggaaaagagttagtatcagcaggatatgacaaatgtctcagaatctttaatgtggacacaactcgcagcagagaagtttacca
# cacaaaaagaatgcaaagggttagggtggtgaaatggtctctagataacaaatatatcatctcaggatcggatgaaatgaatattcgtgtgtggaaag
# ccagggcatcagaaaagcttggaatgataactacaagagagaaagcatccatcaattataatgagaagctaaaagataaattcatgcatcacccacaa
# atcagaaggattgcacgccacagacatgtgcctagacaaatacacagtttgtcaaaggaaatgagaattatgaaggaatcacgcaaacgaaagtga]
# protein sequence = [LYTFDMRKLSAPVMMHMDHVAAVMDVDYSPTGKELVSAGYDKCLRIFNVDTTRSREVYHTKRMQRVRVVKWSLDNKYI
# ISGSDEMNIRVWKARASEKLGMITTREKASINYNEKLKDKFMHHPQIRRIARHRHVPRQIHSLSKEMRIMKESRKRK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AV1.prfl --predictionStart=0  --predictionEnd=24228  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7273320180911_busco_2432604931_.temp