# 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..235]--> unknown_A (14) <--[1..35]--> unknown_B (22) <--[1..37]--> unknown_C (15) <--[29..40]--> unknown_E (34) <--[0..1]--> unknown_F (23) <--[10..110]--> unknown_G (24) <--[10..45]--> unknown_H (17) <--[7..50]--> unknown_I (19) <--[0..1]--> unknown_J (14) <--[0..4]--> unknown_K (18) <--[10..35]--> unknown_L (21) <--[1..15]--> unknown_M (13) <--[20..104]--> unknown_P (20) <--[3..21]--> unknown_Q (15) <--[0..32]--> unknown_R (13) <--[0..1]--> unknown_S (12) <--[0..9]--> unknown_T (26) <--[1..15]--> unknown_U (20) <--[10..26]--> unknown_V (12) <--[0..6]--> unknown_W (19) <--[0..35]--> unknown_X (11) <--[12..21]--> unknown_Z (13) <--[1..15]--> unknown_AA (33) <--[0..7]--> unknown_AB (14) <--[7..49]--> unknown_AC (19) <--[2..21]--> unknown_AD (21) <--[0..20]--> unknown_AE (21) <--[10..30]--> unknown_AG (31) <--[10..63]--> unknown_AI (14) <--[6..59]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig15069120180911_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 = 4966, name = Contig150691) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig150691	AUGUSTUS	gene	1	4774	0.15	+	.	g1
Contig150691	AUGUSTUS	transcript	1	4774	0.15	+	.	g1.t1
Contig150691	AUGUSTUS	intron	1	147	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	intron	157	2446	0.44	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	intron	2585	3588	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	intron	3781	4206	0.57	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	intron	4334	4716	0.3	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	CDS	148	156	0.57	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	CDS	2447	2584	0.78	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	CDS	3589	3780	0.81	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	CDS	4207	4333	0.45	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	CDS	4717	4774	0.33	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig150691	AUGUSTUS	stop_codon	4772	4774	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aaggagcagaggaccactcagagattgcagataaaattgatgactacttgtggattaagttatctcagatccaggtgga
# ttcagacccctccagacagcacggattcaccctgcaaaggctgcagagcctgctctatgaagatttcggagatagtcacttcagtggataccagaatc
# ctttcctgtatttccaagttctcattcttaccgctcagtttgaggcagccattgagttcatgtcgagaattgaccgacttttgtgtcacgctgtacat
# gtggctctcgttttatatgaacttaagatgttgctccttcctcaatctacacaagcacagcttttaaccaaagattcgtctgatgaggggccattgag
# aagactaaactttttccgcctgattaccacgtatactcgtaaatttgaagcaacagacccccgtgaagccctacaatatttttatttcctaaatgtaa
# acaatggagcagcaagattcattcaaacctccgggatcgagaggagacagtaa]
# protein sequence = [GAEDHSEIADKIDDYLWIKLSQIQVDSDPSRQHGFTLQRLQSLLYEDFGDSHFSGYQNPFLYFQVLILTAQFEAAIEF
# MSRIDRLLCHAVHVALVLYELKMLLLPQSTQAQLLTKDSSDEGPLRRLNFFRLITTYTRKFEATDPREALQYFYFLNVNNGAARFIQTSGIERRQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937049Y.prfl --predictionStart=0  --predictionEnd=23731  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig15069120180911_busco_2432604931_.temp