# 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..130]--> unknown_A (7) <--[12..29]--> unknown_C (18) <--[0..16]--> unknown_D (25) <--[2..43]--> unknown_E (41) <--[0..16]--> unknown_F (19) <--[4..38]--> unknown_G (24) <--[18..59]--> unknown_H (26) <--[19..35]--> unknown_K (14) <--[0..2]--> unknown_L (13) <--[4..36]--> unknown_M (13) <--[10..32]--> unknown_N (11) <--[0..2]--> unknown_O (45) <--[0..18]--> unknown_P (46) <--[65..186]--> unknown_V (17) <--[19..79]--> unknown_Y (18) <--[31..177]--> unknown_AA (14) <--[0..9]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig14547720180911_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 = 2995, name = Contig145477) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig145477	AUGUSTUS	gene	1	1680	0.24	+	.	g1
Contig145477	AUGUSTUS	transcript	1	1680	0.24	+	.	g1.t1
Contig145477	AUGUSTUS	intron	1	1497	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig145477	AUGUSTUS	CDS	1498	1680	0.29	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig145477	AUGUSTUS	stop_codon	1678	1680	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gcagacaaggtggatgcttgccttcatcaaatcctgacgaagttggaaccgaatcgccagcatattgcttgtcttggca
# actgggtgctgtaccatacactgcaggccatgatcaattatcttctggctgggtttgaactggagttatacgcaaactatgaataccattatgtttac
# tggtaa]
# protein sequence = [ADKVDACLHQILTKLEPNRQHIACLGNWVLYHTLQAMINYLLAGFELELYANYEYHYVYW]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KM9.prfl --predictionStart=0  --predictionEnd=21677  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig14547720180911_busco_2432604931_.temp