# 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..154]--> unknown_A (11) <--[8..38]--> unknown_C (41) <--[0..1]--> unknown_D (24) <--[2..35]--> unknown_E (14) <--[0..6]--> unknown_F (15) <--[0..168]--> unknown_G (18) <--[0..1]--> unknown_H (35) <--[1..6]--> unknown_I (16) <--[0..27]--> unknown_J (52) <--[0..1]--> unknown_K (25) <--[8..112]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8145220180911_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 = 12974, name = Contig81452) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig81452	AUGUSTUS	gene	635	9500	0.02	+	.	g1
Contig81452	AUGUSTUS	transcript	635	9500	0.02	+	.	g1.t1
Contig81452	AUGUSTUS	start_codon	635	637	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	intron	868	6781	0.03	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	intron	6993	7266	0.2	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	intron	8087	8314	0.68	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	intron	8490	8836	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	CDS	635	867	0.16	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	CDS	6782	6992	0.08	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	CDS	7267	8086	0.51	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	CDS	8315	8489	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	CDS	8837	9500	0.98	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig81452	AUGUSTUS	stop_codon	9498	9500	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgactgcaaacaaactcaaacttaatgatggtaaaactgagataatggtggttgccagtccccacaaccagtgccgtt
# tgacggatatccgtctgaagattggtgaggcaatattaacactagatcgactgttaaaaaccttggtgctgctctggacgctacttatcaatggaagc
# acaagtcagctccgtggtaaggaagatgtacttcaacatcaggagaatctcccaagtagcgttctactttcgtttaaattatttactgccatgcatga
# agatgaagaatttttggatgttctgaagtactgggaatcgcaaaacaatgggatgaataaaaaagataaactgaaatgcatttacagtgttagtaaac
# aatgcaaacttacagaaaaatttgaaacggcagcaagttcggaaagacagaggctgattgtggatgttatgaaagaggcacttatggatgatgacccc
# tttgtacgttattcagctgccatatctttgggagatgccgtaaatcagtttgaaaatacggactttgttcctgcattgttcagcgacatgatttcatc
# tttgttcagtgttcagtgtgaatacagagtgagcctccttgacttttttggacaccaaataacacagacagtaagtgaaaagaactgggtacagcttg
# tgtcgttgatgggaaagcagtggatgcagctatgtagattatgtctcttcgactcttttcttgtccctggacatgaagattcttccgttctgactgag
# aagatatcggacaaggtcgtcatgcattgtcagtttcttcagctgtggaaaagaatcattaaaagatgcgtcaacagcaaacaagaaaatcttatcga
# attcctgaaaccagttataaacttgacatccaagataaaacccaagatttttgaaaataagatgacctttagagctgtgttgaaattaattaatactg
# tggtaagaaatgtaggtgttttttcagaatttgggactgaatttaaggatctaagtgttcagcttggaaaagctttcgtagactgcttctctccagaa
# tggtttgaagaattctcatgtgattttaaagatggatttggaggagagttaacagtaaattcaaataacaaacagaactattcagtcattagaacagt
# ggcaaacatctgcatcaaatttgcctcagctgtacctaaattaggtgagttcctcaagtgcaaagaaatctaccttttgataggtacatatgtagatc
# tgtatgcaagtttgagttcaaccaatgataattttggaactttaacatccctggacacttggatgggtagaactgttggtacgagtttgtttctttgg
# gttcctcatgtttactcagagcaagatgacggatggattgatattttgatggctcttttggagatatacatggaaggaaaggccaggttgcaaaacca
# ggcagactttggtgctactcaggacgcattgaataaaatacaaccacaccagcaattcttactgtttctggacagcacgggattcgatgacaccctga
# tggtggacctcctcgtctccccggagacatgcttcctgttgtatcttactcaatacctcaggctcgtctgctctgaatggacagaatttgtaaacaca
# cacactaaacacaggtcagccaaatcattgaacattggtttagatgaatcaaaggagagcttaaacactgaaaaagaatgcaactctgaggaagaaaa
# gacagacgcatccgtggatgagatacattctggttcagaatccaatatgtctaatgggctggcattgttacagcagtatgaggaggaggaggaagtaa
# tagaagatagcacaacaaagtccgaatgtgacacggagcatgaaaataaagattcagaacttgaaaaagacgaaactgatcattcagaaagttgtgac
# ttgtcacttgctgatgtaagcgcttgtttggatcaaacgatggctgtgttgatccgagttagactgaagatggagaaatacaaggactctagtatcat
# tcaatacaaccctacagttttgattcatttgatcgagaaagtggaagaactttatgaacagtaa]
# protein sequence = [MTANKLKLNDGKTEIMVVASPHNQCRLTDIRLKIGEAILTLDRLLKTLVLLWTLLINGSTSQLRGKEDVLQHQENLPS
# SVLLSFKLFTAMHEDEEFLDVLKYWESQNNGMNKKDKLKCIYSVSKQCKLTEKFETAASSERQRLIVDVMKEALMDDDPFVRYSAAISLGDAVNQFEN
# TDFVPALFSDMISSLFSVQCEYRVSLLDFFGHQITQTVSEKNWVQLVSLMGKQWMQLCRLCLFDSFLVPGHEDSSVLTEKISDKVVMHCQFLQLWKRI
# IKRCVNSKQENLIEFLKPVINLTSKIKPKIFENKMTFRAVLKLINTVVRNVGVFSEFGTEFKDLSVQLGKAFVDCFSPEWFEEFSCDFKDGFGGELTV
# NSNNKQNYSVIRTVANICIKFASAVPKLGEFLKCKEIYLLIGTYVDLYASLSSTNDNFGTLTSLDTWMGRTVGTSLFLWVPHVYSEQDDGWIDILMAL
# LEIYMEGKARLQNQADFGATQDALNKIQPHQQFLLFLDSTGFDDTLMVDLLVSPETCFLLYLTQYLRLVCSEWTEFVNTHTKHRSAKSLNIGLDESKE
# SLNTEKECNSEEEKTDASVDEIHSGSESNMSNGLALLQQYEEEEEVIEDSTTKSECDTEHENKDSELEKDETDHSESCDLSLADVSACLDQTMAVLIR
# VRLKMEKYKDSSIIQYNPTVLIHLIEKVEELYEQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KYZ.prfl --predictionStart=0  --predictionEnd=26378  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8145220180911_busco_2432604931_.temp