# 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..461]--> unknown_A (18) <--[1..7]--> unknown_B (28) <--[4..23]--> unknown_C (45) <--[42..296]--> unknown_E (29) <--[3..87]--> unknown_F (30) <--[1..2]--> unknown_G (23) <--[0..25]--> unknown_H (11) <--[1..2]--> unknown_I (9) <--[13..34]--> unknown_K (20) <--[0..21]--> unknown_L (19) <--[31..322]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig314720180911_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 = 7561, name = Contig3147) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig3147	AUGUSTUS	gene	1054	6896	0.3	+	.	g1
Contig3147	AUGUSTUS	transcript	1054	6896	0.3	+	.	g1.t1
Contig3147	AUGUSTUS	start_codon	1054	1056	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	intron	1109	1790	0.7	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	intron	1901	4763	0.53	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	intron	4833	5472	0.59	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	intron	5920	6839	0.73	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	CDS	1054	1108	0.8	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	CDS	1791	1900	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	CDS	4764	4832	0.57	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	CDS	5473	5919	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	CDS	6840	6896	0.61	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3147	AUGUSTUS	stop_codon	6894	6896	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgctttttcgtaccatacccagctccttggaaatatttcgacaaagttataagggactacaaaagtctatcagcag
# ttgatattcaagtcattgcactgacattccagctggagaaagaaaatgttggaacagatcacataaaaactgtaccagatagcaagatcaaatgggca
# acctccaaagcaatgcttgagaagccaacatctatagcaggattttaccttgcaaaaggaagaacaaatagaactacttcagaatgcacagtaacttc
# tgacttgtcagacttacaagaaaaagatggtcactctacaccaaaagaagatttagctgaccaatcaatcacttctcaaaatgacacatgtgccaacc
# aatcagtgactgacaatatcaaccaatcagaatcaaataaattagagaaggactcttgtgtagattcaacagaaaccaatccaaccgacagcgaagaa
# aaggaggaggagataactgtcactgctgaaatgctcgaagatgcagaggaggatgaaggaattgaggaggatgaagaggatgatgatgacgatgatga
# tggttggataacgcctagcaatattacctctctgaaacagaagatggtcagtcaagaccacgagaaagtggcggtgactgtaggctgtgtaactacag
# attttgcaatgcagatgtcctcattcagaatgggactgactgtgataactctgtggaggggcctggtataa]
# protein sequence = [MCFFVPYPAPWKYFDKVIRDYKSLSAVDIQVIALTFQLEKENVGTDHIKTVPDSKIKWATSKAMLEKPTSIAGFYLAK
# GRTNRTTSECTVTSDLSDLQEKDGHSTPKEDLADQSITSQNDTCANQSVTDNINQSESNKLEKDSCVDSTETNPTDSEEKEEEITVTAEMLEDAEEDE
# GIEEDEEDDDDDDDGWITPSNITSLKQKMVSQDHEKVAVTVGCVTTDFAMQMSSFRMGLTVITLWRGLV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MGF.prfl --predictionStart=0  --predictionEnd=21858  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig314720180911_busco_2432604931_.temp