# 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
# --[10..67]--> unknown_B (26) <--[2..4]--> unknown_C (15) <--[0..3]--> unknown_D (29) <--[1..12]--> unknown_E (51) <--[9..23]--> unknown_G (22) <--[0..24]--> unknown_H (20) <--[0..17]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4461020180911_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 = 17744, name = Contig44610) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig44610	AUGUSTUS	gene	3780	6766	0.46	-	.	g1
Contig44610	AUGUSTUS	transcript	3780	6766	0.46	-	.	g1.t1
Contig44610	AUGUSTUS	stop_codon	3780	3782	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	intron	3897	4944	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	intron	5032	6763	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	CDS	3780	3896	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	CDS	4945	5031	0.69	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	CDS	6764	6766	0.48	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44610	AUGUSTUS	start_codon	6764	6766	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggccttggatgcaaacacctctaaacagctccagaccattctcgagggattcttacagaaaggacagaaactgtacc
# tacagtctgaggttgaccccagtctggtgggtggtatgacggtgaccattggggacaagtttatagacatgtctctgaaatctaagatcaagctctac
# accgacgttctaaagagtgctgctatctaa]
# protein sequence = [MALDANTSKQLQTILEGFLQKGQKLYLQSEVDPSLVGGMTVTIGDKFIDMSLKSKIKLYTDVLKSAAI]
# end gene g1
###
# start gene g2
Contig44610	AUGUSTUS	gene	7326	15775	0.05	+	.	g2
Contig44610	AUGUSTUS	transcript	7326	15775	0.05	+	.	g2.t1
Contig44610	AUGUSTUS	start_codon	7326	7328	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	intron	7595	11244	0.48	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	intron	11408	15368	0.49	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	intron	15548	15645	0.31	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	CDS	7326	7594	0.48	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	CDS	11245	11407	0.96	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	CDS	15369	15547	0.52	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	CDS	15646	15775	0.21	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig44610	AUGUSTUS	stop_codon	15773	15775	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggggccttatttcggccgcctgacagatacgccaaaaatccacttctctagtcactcttttaagacccctcagatcg
# agcttatgtctcatcatctcaacccttacttgacagacttcgagatcctgtgttccacagatcccagcgactgttccattagctgcacgctaatacag
# agccgaggcgtagctaccgtgacaatcgccgtacacctggatgggtctgttaacagaatcattagttatactctgataaagagaaatacgatgtacgt
# tttaatggacgtggatctgtctattccaaactcgagaacagtaatgtcggaagtgagaaaggactttgatgtgattcgcacgaacattgttaggacag
# atcaaccgtttatcaggccgtgtgctacaggccagcagtgccaatttggcgaaatgccaaagctcttcaagctgacgcacaacagcagcacagaagct
# aatcctctcctacagaagacgggagcaagaacaagtgcctgccgatctgaagcttggctacctgtgaaattaccaaagaaagatgaccctttccagtg
# tggcaactggcggggatccattgctgcgtccatccccagcagaccacaccgccaccacttgcgcatcatcatcgcagcagtccatcgaattgcagtct
# ccgattggtacagactatcgttgactttgagaacaggcctcgacagtgttgacagggagaccattcggagctga]
# protein sequence = [MGPYFGRLTDTPKIHFSSHSFKTPQIELMSHHLNPYLTDFEILCSTDPSDCSISCTLIQSRGVATVTIAVHLDGSVNR
# IISYTLIKRNTMYVLMDVDLSIPNSRTVMSEVRKDFDVIRTNIVRTDQPFIRPCATGQQCQFGEMPKLFKLTHNSSTEANPLLQKTGARTSACRSEAW
# LPVKLPKKDDPFQCGNWRGSIAASIPSRPHRHHLRIIIAAVHRIAVSDWYRLSLTLRTGLDSVDRETIRS]
# end gene g2
###
# start gene g3
Contig44610	AUGUSTUS	gene	15838	16149	0.19	+	.	g3
Contig44610	AUGUSTUS	transcript	15838	16149	0.19	+	.	g3.t1
Contig44610	AUGUSTUS	start_codon	15838	15840	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig44610	AUGUSTUS	CDS	15838	16149	0.19	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig44610	AUGUSTUS	stop_codon	16147	16149	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgaggctcgtcctgcagatcatccataacgggcgaagctggactaccccttcagtgagaaccgggagtgaggcaggcg
# catgctggtcacgacaatctcttaatattataggactggataatgaggaaaacaacagagggaagcaacaccccgggcaaacagtgacatcatccaaa
# cctagcggaggaccggttttgcgacacattggcctctttgtccccacaacacgaacatgccacaatccagctcacccagctcgccgaagtggccaaga
# agaccggtctgatccgcattttttaacaccaacgtga]
# protein sequence = [MRLVLQIIHNGRSWTTPSVRTGSEAGACWSRQSLNIIGLDNEENNRGKQHPGQTVTSSKPSGGPVLRHIGLFVPTTRT
# CHNPAHPARRSGQEDRSDPHFLTPT]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370YC4.prfl --predictionStart=0  --predictionEnd=23899  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4461020180911_busco_2432604931_.temp