# 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
# --[63..825]--> unknown_A (19) <--[2..191]--> unknown_B (51) <--[0..1]--> unknown_C (47) <--[8..15]--> unknown_D (24) <--[2..13]--> unknown_E (40) <--[0..1]--> unknown_F (16) <--[1..7]--> unknown_G (15) <--[1..23]--> unknown_H (27) <--[9..100]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig11309820180911_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 = 1106, name = Contig113098) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig113098	AUGUSTUS	gene	1	1106	0.29	-	.	g1
Contig113098	AUGUSTUS	transcript	1	1106	0.29	-	.	g1.t1
Contig113098	AUGUSTUS	intron	1	102	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig113098	AUGUSTUS	intron	341	1106	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig113098	AUGUSTUS	CDS	103	340	0.48	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aaggaagatgaagaggagaagactgacccccagcatgaacaaattaagtccatgatgcagtccctcttcatcaaactgg
# acgcactgtctaacttccagtacacacccaaacctgctgctccagaggtcaagatcgtcacaaacctgccctctatcatgatggaagaggttgctccg
# gtaacccatggcgatggaaccttgctggctccggaggaaatcaaggtatatattatcattg]
# protein sequence = [KEDEEEKTDPQHEQIKSMMQSLFIKLDALSNFQYTPKPAAPEVKIVTNLPSIMMEEVAPVTHGDGTLLAPEEIKVYII
# I]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370H68.prfl --predictionStart=0  --predictionEnd=20325  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig11309820180911_busco_2432604931_.temp