# 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..102]--> unknown_A (15) <--[0..1]--> unknown_B (39) <--[1..2]--> unknown_C (17) <--[0..1]--> unknown_D (30) <--[3..13]--> unknown_E (22) <--[0..5]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6943320180911_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 = 7397, name = Contig69433) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig69433	AUGUSTUS	gene	1	1547	0.38	+	.	g1
Contig69433	AUGUSTUS	transcript	1	1547	0.38	+	.	g1.t1
Contig69433	AUGUSTUS	intron	1	261	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig69433	AUGUSTUS	intron	387	1433	0.41	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig69433	AUGUSTUS	CDS	262	386	0.81	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig69433	AUGUSTUS	CDS	1434	1547	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig69433	AUGUSTUS	stop_codon	1545	1547	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tgactatgaaaatgtcttatgacaatgtgcatggaaagggtctaatcagaaaggaactgcggaagctggtgatcaacct
# cagtagctcagtgggaatcaagggatccgagcaggggctggcttatataatactggaaccgtactctctaacgagcatggtggaaggatcggagaaaa
# gtgattcggccatcagtaaacaggacaatttagacagtttatacgagtacaaccagttctaa]
# protein sequence = [TMKMSYDNVHGKGLIRKELRKLVINLSSSVGIKGSEQGLAYIILEPYSLTSMVEGSEKSDSAISKQDNLDSLYEYNQF]
# end gene g1
###
# start gene g2
Contig69433	AUGUSTUS	gene	5016	7216	0.08	+	.	g2
Contig69433	AUGUSTUS	transcript	5016	7216	0.08	+	.	g2.t1
Contig69433	AUGUSTUS	start_codon	5016	5018	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	intron	5149	5397	0.36	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	intron	5445	7036	0.25	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	CDS	5016	5148	0.41	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	CDS	5398	5444	0.46	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	CDS	7037	7216	0.37	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig69433	AUGUSTUS	stop_codon	7214	7216	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggcttcgataggcgtccctttcaatctggttactccagctttatccgtggcttccaccgctgcgtctcgggcactga
# tcgccttcgtcaatcgcttcacgggcctcctaatgacgagaaaatggcagtacattccaccaatgattaaaatattcgagtttgcatacaatgcattc
# aaggtgtttttcaaagatgagactgtaaaacaggtgaacgttcccacaataaatggagtctttggtattttgccacaacacgtaccaacactcgcagt
# ccttcagcctggtgttgtctcggtggttgtcaacgattcagagaccaagaacatatttggtatgtttatcagatcgatcacatag]
# protein sequence = [MASIGVPFNLVTPALSVASTAASRALIAFVNRFTGLLMTRKWQYIPPMIKIFEFAYNAFKVFFKDETVKQVNVPTING
# VFGILPQHVPTLAVLQPGVVSVVVNDSETKNIFGMFIRSIT]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370VLM.prfl --predictionStart=0  --predictionEnd=27168  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6943320180911_busco_2432604931_.temp