# 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..43]--> unknown_A (19) <--[1..19]--> unknown_B (37) <--[0..5]--> unknown_C (40) <--[2..93]--> unknown_D (38) <--[0..36]--> unknown_E (16) <--[0..1]--> unknown_F (23) <--[0..21]--> unknown_G (22) <--[1..38]--> unknown_H (18) <--[0..9]--> unknown_I (15) <--[0..63]--> unknown_J (33) <--[1..5]--> unknown_K (23) <--[12..86]--> unknown_M (54) <--[0..1]--> unknown_N (54) <--[0..20]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2403320180911_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 = 9204, name = Contig24033) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig24033	AUGUSTUS	gene	6473	8138	0.18	+	.	g1
Contig24033	AUGUSTUS	transcript	6473	8138	0.18	+	.	g1.t1
Contig24033	AUGUSTUS	start_codon	6473	6475	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	intron	6554	7213	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	intron	7322	7598	0.44	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	intron	7704	7847	0.45	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	intron	7998	8105	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	CDS	6473	6553	0.64	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	CDS	7214	7321	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	CDS	7599	7703	0.45	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	CDS	7848	7997	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	CDS	8106	8138	0.52	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig24033	AUGUSTUS	stop_codon	8136	8138	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgctttgaatctaagagttgggatgccttgaatgaaaatattgtattgtttaccaagaaaagagggcagatcaaac
# agtctgtgacaaagatgattcaagaagcctgcacttacgtagagaaaactccaaaccttgacataaaactaaaactgattgacaccttgcgaaccgtc
# acagctggaaagatatatgtagagatagaaagagctcgactaacaagaactttggccaaaatcaaagaagatgcaggaaaaatatcagaagcagccac
# agttttacaggaactacaggtggaaacatttggatcaatggaaaagaaggagaaaattgaattcatcttagaacaaatgaggctctgtctggcaaaga
# aggattatatcagaactcagattatcagcaagaaaattaacaccaagttctttgaagagaaaactaccacagtacccagagtgctttacactgcattt
# tcatga]
# protein sequence = [MCFESKSWDALNENIVLFTKKRGQIKQSVTKMIQEACTYVEKTPNLDIKLKLIDTLRTVTAGKIYVEIERARLTRTLA
# KIKEDAGKISEAATVLQELQVETFGSMEKKEKIEFILEQMRLCLAKKDYIRTQIISKKINTKFFEEKTTTVPRVLYTAFS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GJ7.prfl --predictionStart=0  --predictionEnd=27988  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2403320180911_busco_2432604931_.temp