# 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..143]--> unknown_A (12) <--[2..12]--> unknown_B (16) <--[9..13]--> unknown_D (14) <--[3..7]--> unknown_E (19) <--[1..38]--> unknown_F (25) <--[3..19]--> unknown_G (20) <--[11..32]--> unknown_H (22) <--[0..16]--> unknown_I (22) <--[2..27]--> unknown_J (46) <--[0..446]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2710420180911_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 = 12896, name = Contig27104) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig27104	AUGUSTUS	gene	1303	12287	0.01	+	.	g1
Contig27104	AUGUSTUS	transcript	1303	12287	0.01	+	.	g1.t1
Contig27104	AUGUSTUS	start_codon	1303	1305	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	1388	1497	0.35	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	1607	4053	0.27	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	4121	5527	0.27	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	5619	6215	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	6507	10684	0.7	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	10831	11341	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	11440	11984	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	intron	12060	12205	0.37	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	1303	1387	0.57	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	1498	1606	0.35	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	4054	4120	0.55	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	5528	5618	0.53	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	6216	6506	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	10685	10830	0.73	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	11342	11439	0.79	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	11985	12059	0.51	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	CDS	12206	12287	0.24	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig27104	AUGUSTUS	stop_codon	12285	12287	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggcagattggaaactgcgttacacgatacagttgtccatactgattgctctgtgccaaaatatcaggaagctggcc
# tgtgtgttgtccatactgatgctctgctgccaaatatcaggaagctggcctatgtggtttatgagaaaaatgtgacagaaaattttgtgacgccgacg
# ccgcaagaacgactcaatgacaacagaatattggagcagatcaaagatctggtttttatcagattgaatacaaatgcactaaaggaagtgacatgcgg
# cagattggaaactgcgttacacgacacagttctccacactgatgctctgtgccaaatatcaggaagtggcccgtgtgaaccagtggaaatgcaaatca
# ggcagaggaagtggggttggattggacaaacattgagggagccaccaaccaacaccacacgactgttacgacaggccctgacttggaacccacagggc
# aagagaaagagaggacgtcctagaaacacctggaggcaagacacggaatcagaattgaaagagtatgacaccacctggcaagaagcagcaaaagaagc
# ccagaagttcagaaccctgttcgctggaggactgtcgttgatggcctatgttcctcatggaacgacaggcctaagttggtttgaattaaatttggatc
# aaaggaaactgcgcactccaacaggaaatctctttcaagttcccagtgaacctttggcactagcaatagcaacagaatggaattcacagaaagacata
# ataaaacgacaagccatgcatttgactaccctcagcaacacggtgcttgacaaccccatgcagaggtcacgtaaggacatcatacaggggattctaca
# ctttcttgagacagatacaatactatcaacagaacccccggaattctcagacttacagaaaagagaatgggagccagttgtggagtggctgaggtcca
# ggatgattccttttgatttagaggccatgaaatcaaggatcaacagtcaaggtattaatgacaagatatgctcattactttga]
# protein sequence = [MGRLETALHDTVVHTDCSVPKYQEAGLCVVHTDALLPNIRKLAYVVYEKNVTENFVTPTPQERLNDNRILEQIKDLVF
# IRLNTNALKEVTCGRLETALHDTVLHTDALCQISGSGPCEPVEMQIRQRKWGWIGQTLREPPTNTTRLLRQALTWNPQGKRKRGRPRNTWRQDTESEL
# KEYDTTWQEAAKEAQKFRTLFAGGLSLMAYVPHGTTGLSWFELNLDQRKLRTPTGNLFQVPSEPLALAIATEWNSQKDIIKRQAMHLTTLSNTVLDNP
# MQRSRKDIIQGILHFLETDTILSTEPPEFSDLQKREWEPVVEWLRSRMIPFDLEAMKSRINSQGINDKICSLL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370P7I.prfl --predictionStart=0  --predictionEnd=30797  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2710420180911_busco_2432604931_.temp