# 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..117]--> unknown_A (9) <--[0..2]--> unknown_B (13) <--[0..7]--> unknown_C (107) <--[0..2]--> unknown_D (9) <--[0..1]--> unknown_E (21) <--[0..9]--> unknown_F (70) <--[0..307]--> unknown_G (29) <--[0..59]--> unknown_H (25) <--[23..87]--> unknown_K (21) <--[2..25]--> unknown_L (28) <--[0..197]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4823620180911_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 = 3630, name = Contig48236) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig48236	AUGUSTUS	gene	1	280	0.37	-	.	g1
Contig48236	AUGUSTUS	transcript	1	280	0.37	-	.	g1.t1
Contig48236	AUGUSTUS	intron	1	43	0.54	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48236	AUGUSTUS	CDS	44	280	0.37	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48236	AUGUSTUS	start_codon	278	280	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttttttcagatatctagaccggttgatatattcctgtcccatgactggcccagaggagtgtacaactatggaaatg
# tgaacatgcagctgaaaaagaagcagtttttccaagaggaaatcgaacaagatcgactcggtagtccggcagctaaagatcttctgcatcacatcaag
# ccagattactggtttgctgctcatcttcatgtaaaatttcccgccattgtccagcaccag]
# protein sequence = [MFFQISRPVDIFLSHDWPRGVYNYGNVNMQLKKKQFFQEEIEQDRLGSPAAKDLLHHIKPDYWFAAHLHVKFPAIVQH
# Q]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370N7W.prfl --predictionStart=0  --predictionEnd=20262  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4823620180911_busco_2432604931_.temp