# 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..299]--> unknown_A (29) <--[1..22]--> unknown_B (16) <--[13..60]--> unknown_D (80) <--[0..9]--> unknown_E (32) <--[1..46]--> unknown_F (34) <--[9..25]--> unknown_G (19) <--[0..3]--> unknown_H (21) <--[0..20]--> unknown_I (10) <--[7..9]--> unknown_K (22) <--[0..171]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig197120180911_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 = 21354, name = Contig1971) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1971	AUGUSTUS	gene	3833	10587	0.11	-	.	g1
Contig1971	AUGUSTUS	transcript	3833	10587	0.11	-	.	g1.t1
Contig1971	AUGUSTUS	stop_codon	3833	3835	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	intron	3916	7095	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	intron	7220	10506	0.2	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	CDS	3833	3915	0.75	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	CDS	7096	7219	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	CDS	10507	10587	0.21	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1971	AUGUSTUS	start_codon	10585	10587	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaccgccctactccagtcgcctctctcgacacgcagggatctgaaggacctattctcccggatccccgggtccaca
# cggaagtgtgtacgctgtacttagctgctagtgtaaatggtgacaggatgaatttcgttaatggaataggtcttattgtatgcttatttgggatctca
# attcatgtcatcatgaaagcagtttctggtgaaaagactatggaaatgttaagagccgatgactcagactcagaggagagtgacattttcaatgcaaa
# agtagaccgatga]
# protein sequence = [MDRPTPVASLDTQGSEGPILPDPRVHTEVCTLYLAASVNGDRMNFVNGIGLIVCLFGISIHVIMKAVSGEKTMEMLRA
# DDSDSEESDIFNAKVDR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GK0.prfl --predictionStart=3292  --predictionEnd=43714  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig197120180911_busco_2432604931_.temp