# 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..168]--> unknown_A (38) <--[14..75]--> unknown_B (20) <--[4..12]--> unknown_C (20) <--[0..11]--> unknown_D (37) <--[4..20]--> unknown_E (30) <--[0..17]--> unknown_F (14) <--[10..33]--> unknown_H (11) <--[1..3]--> unknown_I (17) <--[0..1]--> unknown_J (45) <--[0..3]--> unknown_K (25) <--[0..8]--> unknown_L (29) <--[2..15]--> unknown_M (58) <--[10..17]--> unknown_N (22) <--[1..1]--> unknown_O (17) <--[0..2]--> unknown_P (27) <--[0..17]--> unknown_Q (28) <--[0..2]--> unknown_R (47) <--[8..165]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig705120180911_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 = 7787, name = Contig7051) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig7051	AUGUSTUS	gene	1047	5367	0.33	-	.	g1
Contig7051	AUGUSTUS	transcript	1047	5367	0.33	-	.	g1.t1
Contig7051	AUGUSTUS	stop_codon	1047	1049	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	intron	1125	4334	0.58	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	intron	4447	4638	0.9	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	intron	4779	5181	0.85	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	CDS	1047	1124	0.57	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	CDS	4335	4446	0.88	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	CDS	4639	4778	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	CDS	5182	5367	0.62	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig7051	AUGUSTUS	start_codon	5365	5367	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtacatgtcgtacgtgaagaacacaaagtttacatcgccgaccaccatccctctgatcaacttcatgcagatgtcca
# tggtggagatctttgctattgactctgtgcaggcttaccagcatgctttcatctacatcaggcagcaggccatacatctaaggaatgccatcactgtc
# aagaaaaaggagaattgtcaagcagtgtataactggcagtttattcgatgcttggagttctgggttcgattactgagtagcagtcaccccagtgaggc
# cctgaggcccctgatttatcctctaacacagactatcctagggaccataaaattgattcctacggctcgatattaccctctgcgatttcacctgataa
# aagccttgaatcgactctccctagctacagacacctatataccagttctgcccctgattctggagaatctccagccaggtgccttatcaacagagctc
# cccctggttaccagtaatggaaccagtctcaaactgctgctttaa]
# protein sequence = [MYMSYVKNTKFTSPTTIPLINFMQMSMVEIFAIDSVQAYQHAFIYIRQQAIHLRNAITVKKKENCQAVYNWQFIRCLE
# FWVRLLSSSHPSEALRPLIYPLTQTILGTIKLIPTARYYPLRFHLIKALNRLSLATDTYIPVLPLILENLQPGALSTELPLVTSNGTSLKLLL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093706X0.prfl --predictionStart=0  --predictionEnd=25379  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig705120180911_busco_2432604931_.temp