# 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..160]--> unknown_A (6) <--[12..46]--> unknown_B (39) <--[0..1]--> unknown_C (42) <--[1..2]--> unknown_D (14) <--[5..76]--> unknown_E (10) <--[2..53]--> unknown_F (28) <--[1..3]--> unknown_G (8) <--[3..6]--> unknown_H (8) <--[2..20]--> unknown_I (17) <--[3..5]--> unknown_J (7) <--[1..1]--> unknown_K (35) <--[0..53]--> unknown_L (32) <--[0..8]--> unknown_M (18) <--[2..8]--> unknown_N (114) <--[1..24]--> unknown_O (14) <--[0..25]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9399320180911_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 = 8544, name = Contig93993) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig93993	AUGUSTUS	gene	1553	3846	0.15	-	.	g1
Contig93993	AUGUSTUS	transcript	1553	3846	0.15	-	.	g1.t1
Contig93993	AUGUSTUS	stop_codon	1553	1555	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	intron	1938	2679	0.29	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	intron	2712	3774	0.27	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	CDS	1553	1937	0.26	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	CDS	2680	2711	0.55	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	CDS	3775	3846	0.81	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig93993	AUGUSTUS	start_codon	3844	3846	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaggggtatagagtgagcacaatggaggaggggtatagagtggggccaaaaggaggaggggttatagagagtaagg
# caaaaatggaggaggggtataagagagtgctagaagtatcatatcagagtagtgtaatgtatcaggtgcatgctaggcttctgatacgtgtgtttctc
# aatgatgtgtttgatgatatcattgatattagcaaatgtaccaaaaacctttggctagtgataattccaatgtatttaatttcagttcaaagaaacta
# tgatcctaacttgcacccttttgaggccccaagagaatatgtcagggctctgaatgccacgaagttggagcgagtatttgccaaaccttttattgggg
# ctctggatgggcacagggatggtgtaaactgcatgtgcaaacatccaacatcactgagttttttgttgtctggcgcgtgtgatggagaggtgacagtc
# agctttcactctttttga]
# protein sequence = [MEGYRVSTMEEGYRVGPKGGGVIESKAKMEEGYKRVLEVSYQSSVMYQVHARLLIRVFLNDVFDDIIDISKCTKNLWL
# VIIPMYLISVQRNYDPNLHPFEAPREYVRALNATKLERVFAKPFIGALDGHRDGVNCMCKHPTSLSFLLSGACDGEVTVSFHSF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AV1.prfl --predictionStart=0  --predictionEnd=21795  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9399320180911_busco_2432604931_.temp