# 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..122]--> unknown_A (71) <--[0..1]--> unknown_B (8) <--[0..12]--> unknown_C (47) <--[0..49]--> unknown_D (99) <--[0..2]--> unknown_E (15) <--[0..1]--> unknown_F (18) <--[0..3]--> unknown_G (22) <--[6..116]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6981820180911_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 = 3576, name = Contig69818) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig69818	AUGUSTUS	gene	1	2068	0.32	+	.	g1
Contig69818	AUGUSTUS	transcript	1	2068	0.32	+	.	g1.t1
Contig69818	AUGUSTUS	intron	1	400	0.78	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	intron	478	1052	0.59	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	intron	1165	1967	0.92	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	CDS	401	477	0.59	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	CDS	1053	1164	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	CDS	1968	2068	0.53	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig69818	AUGUSTUS	stop_codon	2066	2068	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [caacggttttcaacaatgccaacaaccagatcaatgtgtatggagatgatgtggaagtggactatagaggatatgaagt
# aacagtggaaaatttcatcagagttctcacgggtcgactgccccctagcaccccgagaagtaaacgattgttgtcagatgaacactcaaatgtcttgg
# tttatatgacaggtcatggtggagatgggtttttaaagtttcaagatgcagaagaaatttccaatgtggagctagcggacgcttttgaacaaatgtgg
# cagaagaggaggtaa]
# protein sequence = [TVFNNANNQINVYGDDVEVDYRGYEVTVENFIRVLTGRLPPSTPRSKRLLSDEHSNVLVYMTGHGGDGFLKFQDAEEI
# SNVELADAFEQMWQKRR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370IUA.prfl --predictionStart=0  --predictionEnd=22402  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6981820180911_busco_2432604931_.temp