# 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
# --[41..494]--> unknown_E (61) <--[0..1]--> unknown_F (19) <--[7..22]--> unknown_G (44) <--[0..2]--> unknown_H (22) <--[5..26]--> unknown_I (34) <--[2..5]--> unknown_J (39) <--[0..82]--> unknown_K (39) <--[17..54]--> unknown_M (29) <--[1..18]--> unknown_N (33) <--[0..1]--> unknown_O (21) <--[11..76]--> unknown_P (32) <--[23..51]--> unknown_R (19) <--[0..1]--> unknown_S (10) <--[21..47]--> unknown_U (15) <--[0..2]--> unknown_V (28) <--[4..11]--> unknown_W (21) <--[5..18]--> unknown_X (20) <--[11..35]--> unknown_Y (17) <--[0..498]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig746920180911_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 = 29342, name = Contig7469) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig7469	AUGUSTUS	gene	2194	9399	0.14	+	.	g1
Contig7469	AUGUSTUS	transcript	2194	9399	0.14	+	.	g1.t1
Contig7469	AUGUSTUS	start_codon	2194	2196	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	intron	2223	8070	0.19	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	intron	8171	8277	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	intron	8351	8529	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	intron	8724	9177	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	CDS	2194	2222	0.21	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	CDS	8071	8170	0.65	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	CDS	8278	8350	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	CDS	8530	8723	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	CDS	9178	9399	0.66	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7469	AUGUSTUS	stop_codon	9397	9399	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcgtcaagaaggaaaaaccgatctcagtcacaagcttgcaactaacatcagtgtggaagacatcttggatctgaagt
# tttgtactgatggtgtacagacggctctacagaacgaggattacgaaaaggctgcaggtcatgttcacagatttaggagtttagatgaaaacatttta
# agaatgtcagaagaatccgatgaaggaggcacactggatttgtcctttggacttctacaggaagcagaggaaaaactgaagtccatcgttaacaccaa
# gtttgatgctgctgtccattccggagattttgcctccatagaaagattctttaagatctttccactaattggtctacatgaggaagggctgactaaat
# ttggaaaatttttgtgttcacagatatctgagaaaagtcttggtaatttgaagattgccgagtctatgggcagtcgcgacaagaactctaacgtgatc
# tatgcagagacggccaccaagctgttcgaaggcctagccaatgtggtggaagtgaggcagccattggtggaaacttattttggtatgggtatttgtca
# tatacatatgccaaacttccgccagaggtcgttcctcacgcaaaactaa]
# protein sequence = [MRQEGKTDLSHKLATNISVEDILDLKFCTDGVQTALQNEDYEKAAGHVHRFRSLDENILRMSEESDEGGTLDLSFGLL
# QEAEEKLKSIVNTKFDAAVHSGDFASIERFFKIFPLIGLHEEGLTKFGKFLCSQISEKSLGNLKIAESMGSRDKNSNVIYAETATKLFEGLANVVEVR
# QPLVETYFGMGICHIHMPNFRQRSFLTQN]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093706RN.prfl --predictionStart=0  --predictionEnd=29342  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig746920180911_busco_2432604931_.temp