# 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..47]--> unknown_A (19) <--[1..4]--> unknown_B (10) <--[0..11]--> unknown_C (31) <--[0..32]--> unknown_D (58) <--[0..1]--> unknown_E (43) <--[1..22]--> unknown_F (52) <--[0..3]--> unknown_G (20) <--[0..2]--> unknown_H (24) <--[0..2]--> unknown_I (36) <--[5..37]--> unknown_J (8) <--[0..6]--> unknown_K (8) <--[0..1447]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7901620180911_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 = 5750, name = Contig79016) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig79016	AUGUSTUS	gene	3054	4525	0.06	+	.	g1
Contig79016	AUGUSTUS	transcript	3054	4525	0.06	+	.	g1.t1
Contig79016	AUGUSTUS	start_codon	3054	3056	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	intron	3117	3251	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	intron	3358	4331	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	CDS	3054	3116	0.59	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	CDS	3252	3357	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	CDS	4332	4525	0.13	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig79016	AUGUSTUS	stop_codon	4523	4525	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatagccagactcgggaaggaaattgaccaccctgactctgtctactactgggcccaaaagaacaacattccagtgt
# tttgtccagccctgacggatggttccatcggagacatgatttatttccactcattcaagaaccctggactggtgttggatattgtagaagacattcga
# cgtgtaaacagccaggccgtgcatgctgccaatacaggcatgattattctaggagggggagtcgtcaagcatcacatctgtaatgctaacctgatggt
# aagatatcctgtaatgctagctgaggtaaaagaatatcaacccgtgttaatgctataccctgtgataagatatctgtataatgtttaa]
# protein sequence = [MIARLGKEIDHPDSVYYWAQKNNIPVFCPALTDGSIGDMIYFHSFKNPGLVLDIVEDIRRVNSQAVHAANTGMIILGG
# GVVKHHICNANLMVRYPVMLAEVKEYQPVLMLYPVIRYLYNV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370F47.prfl --predictionStart=0  --predictionEnd=24477  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7901620180911_busco_2432604931_.temp