# 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..372]--> unknown_A (14) <--[3..6]--> unknown_B (40) <--[1..2]--> unknown_C (25) <--[2..3]--> unknown_D (13) <--[0..3]--> unknown_E (46) <--[1..5]--> unknown_F (16) <--[0..4]--> unknown_G (15) <--[0..2]--> unknown_H (24) <--[2..135]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig217020180911_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 = 16846, name = Contig2170) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig2170	AUGUSTUS	gene	1	5123	0.63	+	.	g1
Contig2170	AUGUSTUS	transcript	1	5123	0.63	+	.	g1.t1
Contig2170	AUGUSTUS	intron	1	289	0.74	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	intron	447	2634	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	intron	2739	5039	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	CDS	290	446	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	CDS	2635	2738	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	CDS	5040	5123	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2170	AUGUSTUS	stop_codon	5121	5123	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gatctgtcttatctgaatagagacttgaacaaggtagttatgatagactgcaagtcgacagctgtgaagctgcagcgaa
# ggaacgcgtttgttctaaaagagtgggacggcaaggaggatgacaccactttgtttgacctggcgtcattccttcagacattagcacatagtaaagtg
# gatgatgtccgcacagtgctagattactacatgcagtttgaggatcctattgccaaatttagagaaaaccagctacttcttcaggaggaacaagagag
# actaagacaaattcaggagaaaccaaaacaaaaatcccattttgactttgccaagtcatttagaaagtga]
# protein sequence = [DLSYLNRDLNKVVMIDCKSTAVKLQRRNAFVLKEWDGKEDDTTLFDLASFLQTLAHSKVDDVRTVLDYYMQFEDPIAK
# FRENQLLLQEEQERLRQIQEKPKQKSHFDFAKSFRK]
# end gene g1
###
# start gene g2
Contig2170	AUGUSTUS	gene	11802	16846	0.11	-	.	g2
Contig2170	AUGUSTUS	transcript	11802	16846	0.11	-	.	g2.t1
Contig2170	AUGUSTUS	stop_codon	11802	11804	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	intron	11938	13472	0.46	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	intron	13569	14546	0.5	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	intron	14724	15449	0.54	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	intron	15629	16846	0.52	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	CDS	11802	11937	0.87	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	CDS	13473	13568	0.5	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	CDS	14547	14723	0.57	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig2170	AUGUSTUS	CDS	15450	15628	0.79	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [tgtaaagaaatgatgcgacctgtgaagaaagctttaaaacgtttagataacccagatgagggtttatcggacagggagc
# agttggtgcatactcgacagtgtttgttaaagattggggacaggattaacgagtgtatggctcactataatgacccagaggtcatcaaacagtggaga
# agacgttttcatattcgttttaagggtggaagtacgaagccccagccctctgagaaacatggaaaccatgtagacaaacagagtgagggcaagaaaca
# caaaagaacagcagaatatggggatggggacaaacccaccaaaagaccctcgcatgaacacagggccaaggaacataaaaggtacgacaacagctcaa
# gtgcctatggacgtcagcagcattaccaagacaggagttaccatggcaatgacccccgatttggtgattcacaccacagctaccagtctcattcagat
# aggaagcggaaaagtgatgcagttccagaccgtcgatctcagaaggatcctcgaattctagaagacgccagtcggtcatcgttttattccaactccag
# tcaggatgccaagatttga]
# protein sequence = [CKEMMRPVKKALKRLDNPDEGLSDREQLVHTRQCLLKIGDRINECMAHYNDPEVIKQWRRRFHIRFKGGSTKPQPSEK
# HGNHVDKQSEGKKHKRTAEYGDGDKPTKRPSHEHRAKEHKRYDNSSSAYGRQQHYQDRSYHGNDPRFGDSHHSYQSHSDRKRKSDAVPDRRSQKDPRI
# LEDASRSSFYSNSSQDAKI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TBG.prfl --predictionStart=0  --predictionEnd=20448  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig217020180911_busco_2432604931_.temp