# 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
# --[10..147]--> unknown_B (15) <--[8..27]--> unknown_C (14) <--[1..24]--> unknown_D (19) <--[1..35]--> unknown_E (17) <--[2..34]--> unknown_F (19) <--[4..44]--> unknown_G (16) <--[0..4]--> unknown_H (61) <--[1..68]--> unknown_I (17) <--[2..14]--> unknown_J (26) <--[0..129]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9152720180911_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 = 10432, name = Contig91527) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig91527	AUGUSTUS	gene	1	1849	0.08	-	.	g1
Contig91527	AUGUSTUS	transcript	1	1849	0.08	-	.	g1.t1
Contig91527	AUGUSTUS	intron	1	916	0.43	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig91527	AUGUSTUS	intron	1088	1796	0.89	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig91527	AUGUSTUS	CDS	917	1087	0.96	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig91527	AUGUSTUS	CDS	1797	1849	0.31	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig91527	AUGUSTUS	start_codon	1847	1849	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggatgccgttacacttactgagtacgccgacaagctgtgtggaacgtacagtggtgggaacaagaggaaactgagca
# ctgcgatcgcacttgttggggatcccccgtttctgatgttggacgaacctactaccggggtggatcccgccgcacgacgactggtgtggaacgtctta
# tctaaaatccgagccagtggacggacgcttgtcttaacatcacacag]
# protein sequence = [MDAVTLTEYADKLCGTYSGGNKRKLSTAIALVGDPPFLMLDEPTTGVDPAARRLVWNVLSKIRASGRTLVLTSH]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370K15.prfl --predictionStart=0  --predictionEnd=30418  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9152720180911_busco_2432604931_.temp