# 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..62]--> unknown_A (50) <--[10..30]--> unknown_C (33) <--[2..14]--> unknown_D (48) <--[0..4]--> unknown_E (14) <--[0..14]--> unknown_F (20) <--[0..7]--> unknown_G (9) <--[2..7]--> unknown_H (38) <--[4..12]--> unknown_I (7) <--[0..1]--> unknown_J (11) <--[0..7]--> unknown_K (12) <--[0..212]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3849020180911_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 = 22047, name = Contig38490) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig38490	AUGUSTUS	gene	14233	16287	0.34	+	.	g1
Contig38490	AUGUSTUS	transcript	14233	16287	0.34	+	.	g1.t1
Contig38490	AUGUSTUS	start_codon	14233	14235	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	intron	14271	15844	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	intron	15880	16147	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	CDS	14233	14270	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	CDS	15845	15879	0.61	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	CDS	16148	16287	0.4	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig38490	AUGUSTUS	stop_codon	16285	16287	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttctgtcggacggctcaaatttttgtaccacaatgcacgcaagtgcgtgggatggcgactttgaaagagattcgtc
# tcaggctgaagtcagtcaccaacattcagaaaatcacaaaatcaatgaagatggtgtcagctgcaaaatatgccagagcagagagagagctgaagcct
# gcgaaaccctacggagagcaggccactggtttgtag]
# protein sequence = [MFCRTAQIFVPQCTQVRGMATLKEIRLRLKSVTNIQKITKSMKMVSAAKYARAERELKPAKPYGEQATGL]
# end gene g1
###
# start gene g2
Contig38490	AUGUSTUS	gene	18213	19811	0.32	+	.	g2
Contig38490	AUGUSTUS	transcript	18213	19811	0.32	+	.	g2.t1
Contig38490	AUGUSTUS	start_codon	18213	18215	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	intron	18371	19152	0.96	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	intron	19300	19792	0.65	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	CDS	18213	18370	0.47	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	CDS	19153	19299	0.89	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	CDS	19793	19811	0.65	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig38490	AUGUSTUS	stop_codon	19809	19811	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaaggaggacgaggagacagagatgatcatcgccctgacgtctgaccgaggcctctgtggatcggtccactccagcg
# tggtcaaggcagtcaaagccaggttactagagaaagacgacgccaagctgatcctggtgggagacaaagccaaggccatattacatggaaagaaagtc
# ctaggtcatttcaacgatattggcaaagctcctcccgtgttcggagacgcttcaaagatcgcactggcagctctaaacatgggtctacaggacttcac
# caaagttaccctgtatttcaacacattcaagaaagcgaaaggaatatga]
# protein sequence = [MKEDEETEMIIALTSDRGLCGSVHSSVVKAVKARLLEKDDAKLILVGDKAKAILHGKKVLGHFNDIGKAPPVFGDASK
# IALAALNMGLQDFTKVTLYFNTFKKAKGI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370K1R.prfl --predictionStart=0  --predictionEnd=38377  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3849020180911_busco_2432604931_.temp