# 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..71]--> unknown_A (21) <--[7..16]--> unknown_B (15) <--[1..2]--> unknown_C (21) <--[1..20]--> unknown_D (25) <--[0..1]--> unknown_E (48) <--[3..112]--> unknown_F (25) <--[1..7]--> unknown_G (10) <--[0..35]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig258520180911_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 = 11600, name = Contig2585) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig2585	AUGUSTUS	gene	3160	3699	0.68	+	.	g1
Contig2585	AUGUSTUS	transcript	3160	3699	0.68	+	.	g1.t1
Contig2585	AUGUSTUS	start_codon	3160	3162	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2585	AUGUSTUS	CDS	3160	3699	0.68	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2585	AUGUSTUS	stop_codon	3697	3699	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgccgcgagcaaaggaccgcggggggtgcacaggattaaaagagagggtatgggagagaggaggttggggaatgtgga
# gcatcgagttggcgaaagacgagggacgcgtgaataggggggaccgaggcattacgcagagaggcgggctagagctgggaatgggggtccctgaaagg
# ggaaagcaaagggggggggagaggacgaggaggggaagacgtcgtgcgaggacggaggctggggagagagagaggcagggagcgtggggaaagggaga
# ctggagggagcggggagggggcgaagggagctcgggtagcggaggagagagaaagaggccggtcgaaggagatgagagggaggatgtggagggatcaa
# agcggggtagtggaaagaccagatgggctgccgagggggcaggggggaggagggtgggaagagggagagaggagctgaatgacgggtgttggcggagg
# aggggtgagaggagcgggtggttggagaggggagggggggagtgggggtcgggcgaagagagtgtctag]
# protein sequence = [MPRAKDRGGCTGLKERVWERGGWGMWSIELAKDEGRVNRGDRGITQRGGLELGMGVPERGKQRGGERTRRGRRRARTE
# AGERERQGAWGKGDWRERGGGEGSSGSGGERKRPVEGDEREDVEGSKRGSGKTRWAAEGAGGRRVGRGREELNDGCWRRRGERSGWLERGGGEWGSGE
# ESV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SV2.prfl --predictionStart=0  --predictionEnd=30668  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig258520180911_busco_2432604931_.temp