# 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
# --[14..46]--> unknown_C (35) <--[0..2]--> unknown_D (41) <--[1..4]--> unknown_E (31) <--[0..3]--> unknown_F (12) <--[0..42]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig13517820180911_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 = 2068, name = Contig135178) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig135178	AUGUSTUS	gene	1	2068	0.62	-	.	g1
Contig135178	AUGUSTUS	transcript	1	2068	0.62	-	.	g1.t1
Contig135178	AUGUSTUS	intron	1	629	0.85	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig135178	AUGUSTUS	intron	812	2068	0.73	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig135178	AUGUSTUS	CDS	630	811	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gaattcatgctatgtaagcaggagaacactcagaatccagctgtgtgtttgaaagagggcaaggaagtcacaaggtgcg
# gcttccagttttttggcaaagtaaagaaacactgcctgaaagaatttgaaacctactacaagtgcgtagacagagattacaaaggaactctggatttt
# gccaa]
# protein sequence = [EFMLCKQENTQNPAVCLKEGKEVTRCGFQFFGKVKKHCLKEFETYYKCVDRDYKGTLDFA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093712G8.prfl --predictionStart=0  --predictionEnd=20811  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig13517820180911_busco_2432604931_.temp