# 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
# --[18..68]--> unknown_A (37) <--[20..37]--> unknown_C (18) <--[3..13]--> unknown_D (27) <--[4..6]--> unknown_E (12) <--[10..22]--> unknown_G (10) <--[10..38]--> unknown_I (33) <--[0..1]--> unknown_J (11) <--[11..44]--> unknown_M (16) <--[0..2]--> unknown_N (19) <--[22..38]--> unknown_P (88) <--[55..195]--> unknown_S (18) <--[0..2]--> unknown_T (41) <--[31..88]--> unknown_W (14) <--[0..2]--> unknown_X (17) <--[1..25]--> unknown_Y (20) <--[0..19]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2651920180911_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 = 18756, name = Contig26519) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig26519	AUGUSTUS	gene	4173	5376	0.59	-	.	g1
Contig26519	AUGUSTUS	transcript	4173	5376	0.59	-	.	g1.t1
Contig26519	AUGUSTUS	stop_codon	4173	4175	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26519	AUGUSTUS	intron	4332	5220	0.62	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26519	AUGUSTUS	CDS	4173	4331	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26519	AUGUSTUS	CDS	5221	5376	0.86	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26519	AUGUSTUS	start_codon	5374	5376	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagcgagcccattgaccaagccaaaacgagaacaaccgtcggcactgcccctccgacatccagagacagacaaagcc
# cgtccaagggaacaggagcagcaaagattctctcattaagacttctttcaaggagtgccgtagtccttcacacgtgtattgtctggacaacgaagatt
# gcggtgctgttgtcgcccgctgcctgggacgaagccaaaagactggactctgtcatcgatgacaccacttgtctaatcaggctgtccacactcctcat
# ctatgtgactttctatgaccctgtctctgttcagccttga]
# protein sequence = [MSEPIDQAKTRTTVGTAPPTSRDRQSPSKGTGAAKILSLRLLSRSAVVLHTCIVWTTKIAVLLSPAAWDEAKRLDSVI
# DDTTCLIRLSTLLIYVTFYDPVSVQP]
# end gene g1
###
# start gene g2
Contig26519	AUGUSTUS	gene	11223	15031	0.06	+	.	g2
Contig26519	AUGUSTUS	transcript	11223	15031	0.06	+	.	g2.t1
Contig26519	AUGUSTUS	start_codon	11223	11225	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	11345	11692	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	11883	12659	0.97	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	12816	13301	0.84	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	13327	14082	0.25	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	14307	14512	0.59	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	intron	14609	14932	0.59	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	11223	11344	0.94	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	11693	11882	0.99	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	12660	12815	0.87	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	13302	13326	0.84	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	14083	14306	0.36	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	14513	14608	0.79	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	CDS	14933	15031	0.42	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig26519	AUGUSTUS	stop_codon	15029	15031	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtcgatgggcgacgccttgagagaaattcacgacaagtcggtcattagaagtgactttattcttgtgtatggggaca
# ttgtcgccaacattaggcttcaagatatattaaatgagcacaaaaaacgaagggaagacaaaacttctcccaagaacagaaactcggtgatgaccatg
# attttccagaaagttccaccagggcatcggtcacgcaacaaagaagacgacatcgtcatggcgatagaccagtcgtctgacagggtcctacattacca
# gagagtcacggaacagtctaaactgcagataccagtggaagttttgacagagaatagtaatgtacagctgaggtacgacctgctggacagccagatca
# gtgtctgctcaccagaagttctctccctttacaaggacaactttgattacctcaacagggacgactttgtcaaggggatacttatcaatgaagatata
# atggagaagacaatgcatgtgtttgatgttgatgtagctaatgctggtgttgatgcagctaatgttgatgtagctgatgttggtgtagctaatgctgg
# tgttgatgtagctactgctggtgttgatgtagctaatgttgatgttgatgtagctaacgctaatgttgatgttgatgtagctaatgctaatgttgatg
# ttggtgtagctgatgctgatgtagctgatgctgatgttgatgtagattgtctgatgcttgatgttgatgtggctaatgctgatgttgatgtagctaat
# gttgatgtagataatgctgatgttgatgtggctaatgctgatgttgatctaatgctggtgtttgatgcagctaatgttgatgtagttgatgttgatgt
# agctagatgcttggtgtttgatgtagctaatgctgctgtgttgatgtag]
# protein sequence = [MSMGDALREIHDKSVIRSDFILVYGDIVANIRLQDILNEHKKRREDKTSPKNRNSVMTMIFQKVPPGHRSRNKEDDIV
# MAIDQSSDRVLHYQRVTEQSKLQIPVEVLTENSNVQLRYDLLDSQISVCSPEVLSLYKDNFDYLNRDDFVKGILINEDIMEKTMHVFDVDVANAGVDA
# ANVDVADVGVANAGVDVATAGVDVANVDVDVANANVDVDVANANVDVGVADADVADADVDVDCLMLDVDVANADVDVANVDVDNADVDVANADVDLML
# VFDAANVDVVDVDVARCLVFDVANAAVLM]
# end gene g2
###
# start gene g3
Contig26519	AUGUSTUS	gene	17103	18362	0.2	+	.	g3
Contig26519	AUGUSTUS	transcript	17103	18362	0.2	+	.	g3.t1
Contig26519	AUGUSTUS	start_codon	17103	17105	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	intron	17158	17827	0.44	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	intron	17916	18256	0.9	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	CDS	17103	17157	0.2	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	CDS	17828	17915	0.54	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	CDS	18257	18362	0.87	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig26519	AUGUSTUS	stop_codon	18360	18362	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgttcgactcagcattctatccagtcaaattgggaaaaatcaattttactgtaattcccgatacccagacagatgaac
# gtggtcaaatcatcacccataatcgacataacatctacacaagtgaagatgtcacgctagcaaaaggttgtgtattagagaagaatgttttggtggga
# aggggaactagaattggcagtgacaggcagaataacggactctgtgataggaaaagactgcaaaataggtaa]
# protein sequence = [MFDSAFYPVKLGKINFTVIPDTQTDERGQIITHNRHNIYTSEDVTLAKGCVLEKNVLVGRGTRIGSDRQNNGLCDRKR
# LQNR]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937092T.prfl --predictionStart=0  --predictionEnd=32872  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2651920180911_busco_2432604931_.temp