# 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..152]--> unknown_A (32) <--[0..2]--> unknown_B (35) <--[0..9]--> unknown_C (15) <--[0..24]--> unknown_D (41) <--[0..4]--> unknown_E (9) <--[0..4]--> unknown_F (114) <--[2..54]--> unknown_G (54) <--[0..7]--> unknown_H (8) <--[0..1]--> unknown_I (37) <--[1..12]--> unknown_J (46) <--[0..30]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5511820180911_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 = 18229, name = Contig55118) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig55118	AUGUSTUS	gene	5723	10036	0.29	+	.	g1
Contig55118	AUGUSTUS	transcript	5723	10036	0.29	+	.	g1.t1
Contig55118	AUGUSTUS	start_codon	5723	5725	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	intron	5966	7450	0.4	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	intron	7577	9862	0.83	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	CDS	5723	5965	0.33	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	CDS	7451	7576	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	CDS	9863	10036	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55118	AUGUSTUS	stop_codon	10034	10036	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacgcttcattggttacctgtggcgtatcgaacgatatataagatcatcttgtacaccttcaaggctctacagaaaa
# cagccccagtatacatccaggaactggttcagccacatcggacactacggtctggggattcgatgagccttctaaagccacgcactcatagtagacgt
# tatgttgatagaaggttcgatgtgtcctcagccacactgtggaaactgtctcccaaaagatcttcggtgatactgtgtctgggtgccctgccttttgt
# atggaaactctccggaagaattacgggacattttggatatggtggcgagtatgaggtggatatgcaggatttgtttgtattatactgtagcagcaccc
# tgccctttttcctgaaggacacagtaaagaaactgtttgttggaatggctctagctcttccaatagtctccctcctcatctacatcatcaagatcgga
# ggcgattatttcttcgtctatgcctggggatttatgttagcagtgtctttggtaggtcatatggtcatctag]
# protein sequence = [MTLHWLPVAYRTIYKIILYTFKALQKTAPVYIQELVQPHRTLRSGDSMSLLKPRTHSRRYVDRRFDVSSATLWKLSPK
# RSSVILCLGALPFVWKLSGRITGHFGYGGEYEVDMQDLFVLYCSSTLPFFLKDTVKKLFVGMALALPIVSLLIYIIKIGGDYFFVYAWGFMLAVSLVG
# HMVI]
# end gene g1
###
# start gene g2
Contig55118	AUGUSTUS	gene	12577	14640	0.32	-	.	g2
Contig55118	AUGUSTUS	transcript	12577	14640	0.32	-	.	g2.t1
Contig55118	AUGUSTUS	stop_codon	12577	12579	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	intron	13509	13668	0.58	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	intron	13862	14007	0.57	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	intron	14246	14302	0.64	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	CDS	12577	13508	0.56	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	CDS	13669	13861	0.55	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	CDS	14008	14245	0.64	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	CDS	14303	14640	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55118	AUGUSTUS	start_codon	14638	14640	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagaaccccgcgggccacagaaatgaggggagggaacgggagggcgggggaagccggagtggaggggtggggcaaa
# gcacggcgaagacaacggcagggggggacaaagaggagagggcagtgggggagggagaggggagaagaaggaacgaccagcgggaggagagaaggcgc
# cagggaagccaagccgaaaaggcaggggaggtggaaagaacgagggagaacaaccaacaggggaggagggagggtagggagaagaaggggagaaacag
# gggccgagcgggggcagggggagcgaaaaaaaacccgccagaaggggcaggagaaagcacgggaaccgcgcgggaggatgtgtgcagacggaaagcgc
# ataccgagcctgggaaacgcgcggaaaaaaagaaagtaagaacgcaaacagcaggcaagccggcagaaggagcgggagggataaaaagagaagcagac
# aaagacggacaggggaggggcaggaggagatggacagggctggcgcaaagagaggaacggccaaaaaaaaaagtggtggtgggcaaggaggaagaagg
# gggcaaagacgagagaattagcgcggaaggacgagaaaagagggcgcggaaggacgaaagaaaagatctcggaaggacgagagaaggagcgcgaagga
# cgaggaaaagagcgcggaggacgagagaaaacgagcgcggaatgacgagaaaagagcgcggaaggagagataaggagcgcggaaggacgaatgaggga
# gcgctggaaagacaagaagagcggcgagcaagcaggccaagcaggggacatgaggaaacagataaacacgcgaacggagcggacagcaggaaaagggc
# aggaggaggcaaaagacaaagaaaagagacgacgagaagaggcggcaccagaaagggcacgaggggggaggggactagggagaatggagaaggcgaaa
# acggagccacaaggcgaggggacggaaggaaagacgaccgggtaggcccggcaggtgtggcacggagagggaccagggaggggccgcggcgggacgga
# ggcaggcagggacccgggagaggggcgcgaatgacacatacgagggtcacggacgggaggcgaggacgagggagagcgggcagaaggaggcggacgag
# cggagaaaacaagaggagaggggcgccgaccgcgagagaggggaaaggggggggtcgaagggcgaaggagggaggcgggggggccgcgggggcgggca
# ggccgagacggagaaggaaatgcgaggacggcggcgagaaaggagatagggcgcgcgcgcccgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcggctgc
# gcgcgcggcacacacgcacgcggggcaggagccaaaaggacaaaagaagggcagaaggagggcaaacagcgcacagacgaaacagcaaaagacagagg
# gaagagggagaacgcggagccgggagagacagggagacggggacagcacagaggaagcgcgggaaggcgagaaggaaggagcggaggcggaagaaccn
# nnnnnnnnnnnnnnnnnnnnnnnncttctacaacatacagtttggttaaggggaatgcgatgcttgcagccagcccctcaatcttggtccgtaagtct
# ccatctggcagcggagtgaatttgtcaaacagaggtgcaataaaatcagcgtag]
# protein sequence = [MENPAGHRNEGREREGGGSRSGGVGQSTAKTTAGGDKEERAVGEGEGRRRNDQREERRRQGSQAEKAGEVERTRENNQ
# QGRREGREKKGRNRGRAGAGGAKKNPPEGAGESTGTAREDVCRRKAHTEPGKRAEKKKVRTQTAGKPAEGAGGIKREADKDGQGRGRRRWTGLAQREE
# RPKKKVVVGKEEEGGKDERISAEGREKRARKDERKDLGRTREGARRTRKRARRTRENERGMTRKERGRRDKERGRTNEGALERQEERRASRPSRGHEE
# TDKHANGADSRKRAGGGKRQRKETTRRGGTRKGTRGEGTRENGEGENGATRRGDGRKDDRVGPAGVARRGTREGPRRDGGRQGPGRGARMTHTRVTDG
# RRGRGRAGRRRRTSGENKRRGAPTAREGKGGGRRAKEGGGGAAGAGRPRRRRKCEDGGEKGDRARAPARARARARARGCARGTHARGAGAKRTKEGQK
# EGKQRTDETAKDRGKRENAEPGETGRRGQHRGSAGRREGRSGGGRTXXXXXXXXXSTTYSLVKGNAMLAASPSILVRKSPSGSGVNLSNRGAIKSA]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AL3.prfl --predictionStart=0  --predictionEnd=32703  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5511820180911_busco_2432604931_.temp