# 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..399]--> unknown_A (17) <--[3..18]--> unknown_B (29) <--[1..8]--> unknown_C (20) <--[12..21]--> unknown_E (22) <--[0..6]--> unknown_F (15) <--[1..4]--> unknown_G (12) <--[0..6]--> unknown_H (7) <--[0..9]--> unknown_I (26) <--[0..28]--> unknown_J (87) <--[0..8]--> unknown_K (62) <--[1..2]--> unknown_L (8) <--[2..8]--> unknown_M (26) <--[4..11]--> unknown_N (39) <--[0..1]--> unknown_O (110) <--[0..8]--> unknown_P (6) <--[0..87]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig21822620180911_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 = 4109, name = Contig218226) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig218226	AUGUSTUS	gene	1	3729	0.1	+	.	g1
Contig218226	AUGUSTUS	transcript	1	3729	0.1	+	.	g1.t1
Contig218226	AUGUSTUS	intron	1	267	0.92	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	intron	388	806	0.45	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	intron	828	997	0.47	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	intron	1176	2468	0.3	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	intron	2495	2939	0.65	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	intron	3112	3601	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	268	387	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	807	827	0.48	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	998	1175	0.83	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	2469	2494	0.31	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	2940	3111	0.81	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	CDS	3602	3729	0.75	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig218226	AUGUSTUS	stop_codon	3727	3729	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtggagacccctctgatgaacatgatcccgggaggggccacagctaagcctttcatcactcaccacaatgaactcaaca
# tggacctgtatatgagagtggccccagaactgtatctcaaagtgtatttgattgtgacagagatgttggtagttggtggtattgatagagtatacgag
# attggacgacagttccggaatgaggggatagatttgacccacaacccagagttcactacgtgcgaattttatatggcctacgcggattacgacgacct
# gatgacaatcacggaatctcttcttgcaggtaatctaacaggaaactttgacttcgttgatgctgtcagagttatggttaaacacatcaccgaggtaa
# aagtgacctatcatccggagggtccccgagggccgcgtgggaggtggactacaccccatcctttcaaacgcatcaagcatctgaaggggctcggagga
# gaggttggggtcacattcccaaacacggaaaagtttgactcagaagggacgcgtaaatttttggatgatctatgtgttaagcatcaggttgaatgtcc
# agcaccaaggacagtggcgcgactcctggacaaggtatgtcatgatgaaatggattttacagacttcaaaatataa]
# protein sequence = [VETPLMNMIPGGATAKPFITHHNELNMDLYMRVAPELYLKVYLIVTEMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFT
# TCEFYMAYADYDDLMTITESLLAGNLTGNFDFVDAVRVMVKHITEVKVTYHPEGPRGPRGRWTTPHPFKRIKHLKGLGGEVGVTFPNTEKFDSEGTRK
# FLDDLCVKHQVECPAPRTVARLLDKVCHDEMDFTDFKI]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937066G.prfl --predictionStart=0  --predictionEnd=21174  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig21822620180911_busco_2432604931_.temp