# 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..246]--> unknown_A (22) <--[0..9]--> unknown_B (40) <--[0..71]--> unknown_C (27) <--[1..6]--> unknown_D (34) <--[1..14]--> unknown_E (48) <--[1..21]--> unknown_F (45) <--[18..124]--> unknown_I (10) <--[0..1]--> unknown_J (26) <--[1..5]--> unknown_K (29) <--[8..17]--> unknown_L (28) <--[3..53]--> unknown_M (22) <--[4..47]--> unknown_N (24) <--[1..42]--> unknown_O (39) <--[31..118]--> unknown_Q (23) <--[21..402]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6872120180911_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 = 12138, name = Contig68721) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig68721	AUGUSTUS	gene	503	730	0.8	-	.	g1
Contig68721	AUGUSTUS	transcript	503	730	0.8	-	.	g1.t1
Contig68721	AUGUSTUS	stop_codon	503	505	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68721	AUGUSTUS	CDS	503	730	0.8	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68721	AUGUSTUS	start_codon	728	730	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaccgatcggacgggaggaaattacagtgtatccatcacggagactggagagaggaaggagagagaaactgaatctg
# tatccatcatgagatggaaaagaggaaggaaagaggaatgcaagcatatccatcatgagatggagaagaggaataacagctatccatcacaagattgg
# agagcaaaggaatggaagcatatccatcatgagattggagagcaggaatga]
# protein sequence = [MTDRTGGNYSVSITETGERKERETESVSIMRWKRGRKEECKHIHHEMEKRNNSYPSQDWRAKEWKHIHHEIGEQE]
# end gene g1
###
# start gene g2
Contig68721	AUGUSTUS	gene	835	1152	0.53	-	.	g2
Contig68721	AUGUSTUS	transcript	835	1152	0.53	-	.	g2.t1
Contig68721	AUGUSTUS	stop_codon	835	837	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig68721	AUGUSTUS	CDS	835	1152	0.53	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig68721	AUGUSTUS	start_codon	1150	1152	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagagaggaatgaagcatatccatcatgagatggaaagaggaataaagtgtatccatcacaagatggagagaggaa
# tgaagcatatccatcatgagatggatgggaggaatgaagtgtatccatcacaagatggacgggagaaggacgagaggaatgagtgctatccatcacaa
# agactggacgagcaggacatgaacgcacattccatacatgagatggaggcgaggaatgaagcatatccatcaggacatggagacagaatgaagcatat
# ccatcatgagatggagggaggaatgaaggtgtatccatcatga]
# protein sequence = [MERGMKHIHHEMERGIKCIHHKMERGMKHIHHEMDGRNEVYPSQDGREKDERNECYPSQRLDEQDMNAHSIHEMEARN
# EAYPSGHGDRMKHIHHEMEGGMKVYPS]
# end gene g2
###
# start gene g3
Contig68721	AUGUSTUS	gene	1846	2493	0.73	-	.	g3
Contig68721	AUGUSTUS	transcript	1846	2493	0.73	-	.	g3.t1
Contig68721	AUGUSTUS	stop_codon	1846	1848	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig68721	AUGUSTUS	intron	2072	2485	0.73	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig68721	AUGUSTUS	CDS	1846	2071	0.77	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig68721	AUGUSTUS	CDS	2486	2493	0.78	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig68721	AUGUSTUS	start_codon	2491	2493	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggaaaaaaattatcatcaaaacccatggttgattacacttctttcctccctccatcacgagattatgggatggagag
# aagaacaagcatatccatcaccagatggagagaagaataaagcagtgtccatcacaagaaggagagaggaatcgcagaggaatgaagcatatccatca
# gaacatggaagagaggaaatgaaggtcatatccatcattgagatggaggaggaatga]
# protein sequence = [MEKNYHQNPWLITLLSSLHHEIMGWREEQAYPSPDGEKNKAVSITRRREESQRNEAYPSEHGREEMKVISIIEMEEE]
# end gene g3
###
# start gene g4
Contig68721	AUGUSTUS	gene	5064	8783	0.06	+	.	g4
Contig68721	AUGUSTUS	transcript	5064	8783	0.06	+	.	g4.t1
Contig68721	AUGUSTUS	start_codon	5064	5066	.	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	intron	5166	5458	0.97	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	intron	5591	8317	0.3	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	intron	8426	8726	0.22	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	CDS	5064	5165	0.9	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	CDS	5459	5590	0.98	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	CDS	8318	8425	0.85	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	CDS	8727	8783	0.25	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig68721	AUGUSTUS	stop_codon	8781	8783	.	+	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atggatgccgctttactgactaccataactgaaatccaagacctcagtcacagaatgttcttcaacagccttaactgcc
# atgctaacaaactactagacaaggtggaattgccccctgctgatctttcaaccccagcagctcttggtcaaaccatgcatctcttaaaggatgttctt
# gcctgtcatgatgcttctgttgtggcaatagatgacaagaaacaggactttaaacaggtggatgctcagctagacactcttgttaatgagcaggcagc
# tacagtcctcaatcgggtgggactcgcagcagcatacagaactgtacaatcttaccaaactaaacaggaaaaacccctgaagagccgagaagtcggag
# gacatcttgtaacattcaatttgtga]
# protein sequence = [MDAALLTTITEIQDLSHRMFFNSLNCHANKLLDKVELPPADLSTPAALGQTMHLLKDVLACHDASVVAIDDKKQDFKQ
# VDAQLDTLVNEQAATVLNRVGLAAAYRTVQSYQTKQEKPLKSREVGGHLVTFNL]
# end gene g4
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093704GD.prfl --predictionStart=0  --predictionEnd=26117  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6872120180911_busco_2432604931_.temp