# 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
# --[36..164]--> unknown_C (38) <--[1..20]--> unknown_D (27) <--[5..39]--> unknown_E (28) <--[5..80]--> unknown_F (41) <--[2..62]--> unknown_G (11) <--[0..14]--> unknown_H (14) <--[0..1]--> unknown_I (28) <--[6..33]--> unknown_J (32) <--[0..500]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2027820180911_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 = 8089, name = Contig20278) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig20278	AUGUSTUS	gene	5996	7968	0.24	+	.	g1
Contig20278	AUGUSTUS	transcript	5996	7968	0.24	+	.	g1.t1
Contig20278	AUGUSTUS	start_codon	5996	5998	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	intron	6109	7252	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	intron	7399	7906	0.4	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	CDS	5996	6108	0.5	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	CDS	7253	7398	0.54	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	CDS	7907	7968	0.41	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig20278	AUGUSTUS	stop_codon	7966	7968	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgattcagaaggccgtatttggtgccggctatcccagcattcccacattgacgattgaggagttctacgaacagaaag
# tgaaagacggcaccttccaggcacctacctcacagggacacagtatgcaagactgggcaggggacccagagaaagataaagaggaccaggagagggag
# gcagaggaaaaggaacagaaaatagagcgtgacgaccccgaggagttacagaagaccagggcgttcgacgactggaaagacgagccaacaggcatctt
# accatttggcgatttgaacattttgcttctaaaattgttacagtga]
# protein sequence = [MIQKAVFGAGYPSIPTLTIEEFYEQKVKDGTFQAPTSQGHSMQDWAGDPEKDKEDQEREAEEKEQKIERDDPEELQKT
# RAFDDWKDEPTGILPFGDLNILLLKLLQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370LQ2.prfl --predictionStart=0  --predictionEnd=26097  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2027820180911_busco_2432604931_.temp