# 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
# --[29..212]--> unknown_B (27) <--[22..69]--> unknown_D (19) <--[0..26]--> unknown_E (21) <--[2..25]--> unknown_F (69) <--[0..1]--> unknown_G (23) <--[0..2]--> unknown_H (10) <--[0..9]--> unknown_I (23) <--[0..1]--> unknown_J (33) <--[0..9]--> unknown_K (38) <--[1..24]--> unknown_L (61) <--[0..69]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9654120180911_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 = 2947, name = Contig96541) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig96541	AUGUSTUS	gene	587	1383	0.84	+	.	g1
Contig96541	AUGUSTUS	transcript	587	1383	0.84	+	.	g1.t1
Contig96541	AUGUSTUS	start_codon	587	589	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig96541	AUGUSTUS	intron	730	1148	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig96541	AUGUSTUS	CDS	587	729	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig96541	AUGUSTUS	CDS	1149	1383	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig96541	AUGUSTUS	stop_codon	1381	1383	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctgcattcagcggcagccatattgaaaatcgcagaaatggactacaatggagctaacagtatttttttgaagacgc
# tgctggacaaaaagtacgccttgccatatcgagttgtggacgccgtggtgtttcactttctcgggttccagagggataagcgagaacttcctgtgttg
# tggcaccagtcgcttctgacctttgttcagcggtacaaggaggatatttctagtgaacaaaaagaggctcttatggatttgttacgagctcaaactca
# cagtcagatcacaccagagattcggcgggaacttgtccacgcgaagtgtcgggacgtagaaggggagccacctggtggtagtggtgcgatggaagatg
# attga]
# protein sequence = [MLHSAAAILKIAEMDYNGANSIFLKTLLDKKYALPYRVVDAVVFHFLGFQRDKRELPVLWHQSLLTFVQRYKEDISSE
# QKEALMDLLRAQTHSQITPEIRRELVHAKCRDVEGEPPGGSGAMEDD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E4W.prfl --predictionStart=0  --predictionEnd=21314  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9654120180911_busco_2432604931_.temp