# 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..216]--> unknown_A (18) <--[4..17]--> unknown_B (22) <--[1..2]--> unknown_C (15) <--[15..45]--> unknown_D (14) <--[1..30]--> unknown_E (31) <--[0..1]--> unknown_F (15) <--[0..6]--> unknown_G (19) <--[4..22]--> unknown_H (14) <--[0..2]--> unknown_I (22) <--[0..17]--> unknown_J (19) <--[1..12]--> unknown_K (13) <--[0..2]--> unknown_L (20) <--[0..14]--> unknown_M (38) <--[1..20]--> unknown_N (20) <--[16..79]--> unknown_O (15) <--[0..46]--> unknown_P (31) <--[15..631]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig11893920180911_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 = 2317, name = Contig118939) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig118939	AUGUSTUS	gene	1	2166	0.56	+	.	g1
Contig118939	AUGUSTUS	transcript	1	2166	0.56	+	.	g1.t1
Contig118939	AUGUSTUS	intron	1	1932	0.57	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig118939	AUGUSTUS	CDS	1933	2166	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig118939	AUGUSTUS	stop_codon	2164	2166	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ggtcaggtgtccatacctgggacggtgggtgcagtcgtggttgagcgaccagcagatgtagaagaaggtttccacctga
# acgctccattggttttccattatggtcacacgtccccctccaccaaccctcagctgtacaaactactggtgtccagaatggccgaggtcaccaacatg
# aaatgtgacaagcaacgcaaaggtcatttcctgtttactcacaatatttgcgcttag]
# protein sequence = [GQVSIPGTVGAVVVERPADVEEGFHLNAPLVFHYGHTSPSTNPQLYKLLVSRMAEVTNMKCDKQRKGHFLFTHNICA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BQO.prfl --predictionStart=0  --predictionEnd=22130  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig11893920180911_busco_2432604931_.temp