# 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..194]--> unknown_A (12) <--[1..32]--> unknown_B (56) <--[0..60]--> unknown_C (61) <--[12..92]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig4835320180911_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 = 8959, name = Contig48353) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig48353	AUGUSTUS	gene	104	2055	0.01	-	.	g1
Contig48353	AUGUSTUS	transcript	104	2055	0.01	-	.	g1.t1
Contig48353	AUGUSTUS	tts	104	104	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	exon	104	467	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	stop_codon	277	279	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	intron	468	660	0.91	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	intron	866	1504	0.78	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	CDS	277	467	0.72	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	CDS	661	865	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	exon	661	865	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	CDS	1505	1516	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	exon	1505	1532	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	start_codon	1514	1516	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	exon	1789	2055	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48353	AUGUSTUS	tss	2055	2055	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacactgttggtttatgaaggactgaagtataagctaaccttggagtttccctgtggatatccttaccaggccccga
# cagtgaaatttgataccccctgctatcaccccaatgtcgaccagagcgggaatatctgtctcgacatcctcaaagagaagtggtcagctctgtacgac
# gttagaacgatacttctatccattcaaagtctgcttggagtgaccgtggtcccacagccaacggtcaggggtcccgagtccactcgtgaccgtggtgc
# cacagccacgtcagatggtcccgagtccagagtgacccgtctggtcccacaagccacgtcaggggtcctgagtcctactaggacccgtggtcccaaca
# gccacgaggtggactcaggacccctgacattgtga]
# protein sequence = [MTLLVYEGLKYKLTLEFPCGYPYQAPTVKFDTPCYHPNVDQSGNICLDILKEKWSALYDVRTILLSIQSLLGVTVVPQ
# PTVRGPESTRDRGATATSDGPESRVTRLVPQATSGVLSPTRTRGPNSHEVDSGPLTL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UID.prfl --predictionStart=0  --predictionEnd=20862  --species=fly ./tmp/Contig4835320180911_busco_2432604931_.temp