# 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
# --[1..79]--> unknown_A (70) <--[13..35]--> unknown_C (35) <--[0..12]--> unknown_D (38) <--[1..11]--> unknown_E (34) <--[11..20]--> unknown_G (9) <--[0..35]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig591920180911_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 = 8133, name = Contig5919) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5919	AUGUSTUS	gene	1	879	0.26	-	.	g1
Contig5919	AUGUSTUS	transcript	1	879	0.26	-	.	g1.t1
Contig5919	AUGUSTUS	intron	1	127	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5919	AUGUSTUS	intron	212	696	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5919	AUGUSTUS	CDS	128	211	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5919	AUGUSTUS	CDS	697	879	0.27	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5919	AUGUSTUS	start_codon	877	879	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaatgcagttattgatgttacagatgaaggaaatcttgagagtcaagtgacagaatccatatctgctgagaaaagag
# tggactcagatgtgggtgaaaattctgtaaccgatccagatgtgggtggacattctacaacagatccagaggaggatgaaatatccagcatcgatcca
# gcaatgaaccagcagttcctcattgagtctgtccagcaggagaacgccaagtttacagactgtaaagacatggaggagatcagtcataca]
# protein sequence = [MNAVIDVTDEGNLESQVTESISAEKRVDSDVGENSVTDPDVGGHSTTDPEEDEISSIDPAMNQQFLIESVQQENAKFT
# DCKDMEEISHT]
# end gene g1
###
# start gene g2
Contig5919	AUGUSTUS	gene	3972	8097	0.02	+	.	g2
Contig5919	AUGUSTUS	transcript	3972	8097	0.02	+	.	g2.t1
Contig5919	AUGUSTUS	start_codon	3972	3974	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	intron	4028	4524	0.17	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	intron	4576	5509	0.38	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	intron	5717	6886	0.53	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	intron	7034	8012	0.3	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	CDS	3972	4027	0.26	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	CDS	4525	4575	0.27	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	CDS	5510	5716	0.68	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	CDS	6887	7033	0.42	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	CDS	8013	8097	0.3	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig5919	AUGUSTUS	stop_codon	8095	8097	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaggcccgattcgtttgtcaggtgtttcgacccatggaatgttcgacccttaaggacaaatagatacaaaccagctt
# cacagatcggggcagccaaaaggacactagccccaacagtgaccggaacctcagtccttggtctgtgttttgatggaggtgtgataatagcagctgac
# atgctcgggtcgtatggctccttggcccgctacaggaatctctcccgcgtgatgaaagtcaacgacaccactgcgctgggtataagcggtgactacgc
# ggattaccagttcatgaaatccataattgaacaaagagttatagacgaggagtgtttaaatgatggattccagtacacacccaagagtctgttttcct
# ggatgacgagggtactatataacaggaggtccaacttcaacccactgtggaatacatttgttgtgggtggaattcaagatggagaaccctcaatgcac
# gttctattgcccgaggcatcagccgagggcattgagctgttcccaataccgagggaaaaatattccgatctataa]
# protein sequence = [MRPDSFVRCFDPWNVRPLRTNRYKPASQIGAAKRTLAPTVTGTSVLGLCFDGGVIIAADMLGSYGSLARYRNLSRVMK
# VNDTTALGISGDYADYQFMKSIIEQRVIDEECLNDGFQYTPKSLFSWMTRVLYNRRSNFNPLWNTFVVGGIQDGEPSMHVLLPEASAEGIELFPIPRE
# KYSDL]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MDU.prfl --predictionStart=0  --predictionEnd=27025  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig591920180911_busco_2432604931_.temp