# 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..36]--> unknown_A (15) <--[1..35]--> unknown_B (71) <--[3..20]--> unknown_C (38) <--[8..23]--> unknown_E (12) <--[0..92]--> unknown_F (26) <--[0..101]--> unknown_G (9) <--[1..17]--> unknown_H (20) <--[1..17]--> unknown_I (24) <--[0..16]--> unknown_J (14) <--[0..36]--> unknown_K (16) <--[6..69]--> unknown_L (15) <--[9..66]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig8414320180911_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 = 4449, name = Contig84143) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig84143	AUGUSTUS	gene	2286	4331	0.06	+	.	g1
Contig84143	AUGUSTUS	transcript	2286	4331	0.06	+	.	g1.t1
Contig84143	AUGUSTUS	tss	2286	2286	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	exon	2286	2372	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	exon	2507	2587	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	start_codon	2516	2518	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	intron	2588	2925	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	CDS	2516	2587	0.57	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	CDS	2926	3063	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	exon	2926	4331	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	stop_codon	3061	3063	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84143	AUGUSTUS	tts	4331	4331	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaactgatggagaaagtattgaacgccttcaagcctggaaaattcctgatgactgtgtttgcaaacaaggaatcga
# ttgccaaggacagctacaagcagctggaggataaagactacgtccccggttatatcagggccgaccaccagtactgtaccttcaagaattacaatctg
# acctactcccacttcacccgacctatcatctag]
# protein sequence = [MELMEKVLNAFKPGKFLMTVFANKESIAKDSYKQLEDKDYVPGYIRADHQYCTFKNYNLTYSHFTRPII]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CKL.prfl --predictionStart=0  --predictionEnd=20943  --species=fly ./tmp/Contig8414320180911_busco_2432604931_.temp