# 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..7]--> unknown_A (14) <--[1..4]--> unknown_B (44) <--[0..2]--> unknown_C (75) <--[1..12]--> unknown_D (10) <--[8..14]--> unknown_F (27) <--[9..46]--> unknown_H (19) <--[8..133]--> unknown_I (18) <--[10..801]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5033320180911_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 = 10205, name = Contig50333) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig50333	AUGUSTUS	gene	1779	3984	0.17	-	.	g1
Contig50333	AUGUSTUS	transcript	1779	3984	0.17	-	.	g1.t1
Contig50333	AUGUSTUS	stop_codon	1779	1781	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig50333	AUGUSTUS	intron	1978	3907	0.79	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig50333	AUGUSTUS	CDS	1779	1977	0.38	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig50333	AUGUSTUS	CDS	3908	3984	0.4	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig50333	AUGUSTUS	start_codon	3982	3984	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgtcggaatcccatcagagacagctgttactgtttgcagaaaacccggataaatacattgatgacttctcaaaag
# aatttatggacgattatctagagcttctgagtaggagatttggtaccaagcgagtccactgtaacatcgtgtatcaggaatacatctcgttccgcgaa
# cacgtccacatgaatgccacacaatgggaatcattgacggaattcgttaaatggctcggcagagaaggtatgacaccactacaatgcaacgaggaata
# g]
# protein sequence = [MMSESHQRQLLLFAENPDKYIDDFSKEFMDDYLELLSRRFGTKRVHCNIVYQEYISFREHVHMNATQWESLTEFVKWL
# GREGMTPLQCNEE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370XFJ.prfl --predictionStart=0  --predictionEnd=24425  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5033320180911_busco_2432604931_.temp