# 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..372]--> unknown_A (14) <--[3..6]--> unknown_B (40) <--[1..2]--> unknown_C (25) <--[2..3]--> unknown_D (13) <--[0..3]--> unknown_E (46) <--[1..5]--> unknown_F (16) <--[0..4]--> unknown_G (15) <--[0..2]--> unknown_H (24) <--[2..135]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig21095120180911_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 = 1260, name = Contig210951) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig210951	AUGUSTUS	gene	1	1260	0.53	+	.	g1
Contig210951	AUGUSTUS	transcript	1	1260	0.53	+	.	g1.t1
Contig210951	AUGUSTUS	intron	1	222	0.9	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig210951	AUGUSTUS	intron	331	513	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig210951	AUGUSTUS	intron	613	1260	0.55	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig210951	AUGUSTUS	CDS	223	330	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig210951	AUGUSTUS	CDS	514	612	0.63	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [attaagaatggctggcggtttaagaagcgaccaggtgtagattatttccttcaggcgatcggcccgcctctgtttgaga
# cagtggtgtacacatcggagacaaacatgaatgccgttcctgtgatccacggccttgaccaacaaggacatatcatgtacaagttatacagagatgcc
# acattgtatgacggcaaagatcatgtgaag]
# protein sequence = [IKNGWRFKKRPGVDYFLQAIGPPLFETVVYTSETNMNAVPVIHGLDQQGHIMYKLYRDATLYDGKDHVK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TBG.prfl --predictionStart=0  --predictionEnd=20357  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig21095120180911_busco_2432604931_.temp