# 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
# --[8..521]--> unknown_A (25) <--[10..47]--> unknown_C (17) <--[1..48]--> unknown_D (14) <--[0..7]--> unknown_E (24) <--[9..24]--> unknown_G (54) <--[11..40]--> unknown_H (12) <--[1..6]--> unknown_I (32) <--[2..66]--> unknown_J (27) <--[0..1]--> unknown_K (21) <--[14..529]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2061720180911_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 = 10918, name = Contig20617) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig20617	AUGUSTUS	gene	4077	5024	0.47	-	.	g1
Contig20617	AUGUSTUS	transcript	4077	5024	0.47	-	.	g1.t1
Contig20617	AUGUSTUS	stop_codon	4077	4079	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig20617	AUGUSTUS	CDS	4077	5024	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig20617	AUGUSTUS	start_codon	5022	5024	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagccggaagagacgtacgattatgcgcatatagacggcggaaacattgcttcatacatggcctcagagaaaggtt
# gtgatactcattcaggagaagttttgcagatgttttgttgcacttgcgaggcggccatctgtgtcacgtgtgtctgtgaatttcacaagaaacatgaa
# acaatgcctttaataaagaaattgatggcgtcccagaaggaactgcagtttgatctcgatgatctaaaaacggaagtaaaactaacacaagattcttt
# atcagatttacgcaatcttcgagcaaaaatacaggagagtaccgacgccacgacgacatcaattcgactacgatcacgtgatcttgcgatggaaatgg
# atcgagtagcggagctaaaaatagaaaaggttcggggtacaactaataaggtccttcaggagatcgacagctacattaaagaactggaacagcttcac
# gaacaagcaaggaagggttgtggattcttggaagatctccaagaagatgacgtcagtttggaattatttgcgtgctttaccaaatataagaaaggatt
# agaggtcgtccgaaagtccgcgctaaacaaaactgtacaaacacagatttcaaatttcaaagctggaaaggtgaagcagttctttggatatcactttt
# tgaagtttggtgatctaaaaatattcaaagacaatgcagtgtttttgaaagtggaaaaggaaccacgattttcaaggtcttccaaatgtcgcaaaatg
# tgctcggttataccggcaatgttatacgtagtactttttgcaattgttatctctggcctatttattttgaccaataatttgtggagttctgatcatgt
# gtctcttgaaggctgcgttggttggcttttcttcttacatctcactatcaccggcgcttttgctttctacaagtcgagaagataa]
# protein sequence = [MEPEETYDYAHIDGGNIASYMASEKGCDTHSGEVLQMFCCTCEAAICVTCVCEFHKKHETMPLIKKLMASQKELQFDL
# DDLKTEVKLTQDSLSDLRNLRAKIQESTDATTTSIRLRSRDLAMEMDRVAELKIEKVRGTTNKVLQEIDSYIKELEQLHEQARKGCGFLEDLQEDDVS
# LELFACFTKYKKGLEVVRKSALNKTVQTQISNFKAGKVKQFFGYHFLKFGDLKIFKDNAVFLKVEKEPRFSRSSKCRKMCSVIPAMLYVVLFAIVISG
# LFILTNNLWSSDHVSLEGCVGWLFFLHLTITGAFAFYKSRR]
# end gene g1
###
# start gene g2
Contig20617	AUGUSTUS	gene	9171	10012	0.79	+	.	g2
Contig20617	AUGUSTUS	transcript	9171	10012	0.79	+	.	g2.t1
Contig20617	AUGUSTUS	start_codon	9171	9173	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig20617	AUGUSTUS	intron	9489	9949	0.94	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig20617	AUGUSTUS	CDS	9171	9488	0.87	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig20617	AUGUSTUS	CDS	9950	10012	0.91	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig20617	AUGUSTUS	stop_codon	10010	10012	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggccagtcttgcaaagcatatattcaagacaacagttgggatgttgccatggatattgtggtggtttctgggaaatg
# tagacattgtttatggttcctatggagataggtcctacatttatcaaaagtgcctgaaaaattgccagttcgagaactgttctaaagcatcgtccatc
# tcgcgcttcaaggagagacagacctggtttgaggaaaaattgcagtggacgtgtgaggatgagtgccagtatcagtgcatgtggatcacagtagaggc
# attccaaaaggatgacatagccattccacagttccatggaaagtggccgtttttgcgggtgttgaggattcaggtgcctggcactgccagcgtctgtt
# gtatctga]
# protein sequence = [MASLAKHIFKTTVGMLPWILWWFLGNVDIVYGSYGDRSYIYQKCLKNCQFENCSKASSISRFKERQTWFEEKLQWTCE
# DECQYQCMWITVEAFQKDDIAIPQFHGKWPFLRVLRIQVPGTASVCCI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KWF.prfl --predictionStart=0  --predictionEnd=30190  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2061720180911_busco_2432604931_.temp