# 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..340]--> unknown_A (29) <--[10..34]--> unknown_C (8) <--[9..17]--> unknown_E (31) <--[3..39]--> unknown_F (12) <--[0..1]--> unknown_G (31) <--[1..32]--> unknown_H (19) <--[2..61]--> unknown_I (27) <--[0..103]--> unknown_J (20) <--[9..72]--> unknown_K (21) <--[0..3]--> unknown_L (8) <--[0..38]--> unknown_M (31) <--[0..172]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7913920180911_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 = 16450, name = Contig79139) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig79139	AUGUSTUS	gene	8521	14731	0.14	+	.	g1
Contig79139	AUGUSTUS	transcript	8521	14731	0.14	+	.	g1.t1
Contig79139	AUGUSTUS	start_codon	8521	8523	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig79139	AUGUSTUS	intron	8567	14495	0.71	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig79139	AUGUSTUS	CDS	8521	8566	0.26	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig79139	AUGUSTUS	CDS	14496	14731	0.66	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig79139	AUGUSTUS	stop_codon	14729	14731	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcctcaagattcggcagccagactgggatggtcacaatgtttaggtaacttgcaggccccctgtgggtacgataaat
# tcagttactcctttcgttcacgacgaggaacgagattccatcagagtcgagggaagcattactgtgatgggggatatgctgagggggacatcatcgga
# ttcttcatccacctacctgagccagacaaccccggcaaactcctgcccaacaccttcaaggaccgggtaagctttaaactatgtcaaggtcaggataa
# gcattag]
# protein sequence = [MPQDSAARLGWSQCLGNLQAPCGYDKFSYSFRSRRGTRFHQSRGKHYCDGGYAEGDIIGFFIHLPEPDNPGKLLPNTF
# KDRVSFKLCQGQDKH]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BYX.prfl --predictionStart=0  --predictionEnd=34704  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7913920180911_busco_2432604931_.temp