# 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..320]--> unknown_A (33) <--[1..36]--> unknown_B (66) <--[0..1]--> unknown_C (54) <--[1..32]--> unknown_D (21) <--[0..1]--> unknown_E (24) <--[0..2]--> unknown_F (19) <--[8..15]--> unknown_G (23) <--[1..23]--> unknown_H (30) <--[0..93]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig18924720180911_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 = 6298, name = Contig189247) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig189247	AUGUSTUS	gene	5397	6298	0.74	-	.	g1
Contig189247	AUGUSTUS	transcript	5397	6298	0.74	-	.	g1.t1
Contig189247	AUGUSTUS	stop_codon	5397	5399	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig189247	AUGUSTUS	intron	5822	6298	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig189247	AUGUSTUS	CDS	5397	5821	0.74	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtgcttggatcatggcagccatcatgttttgctggcagtttccccattttaacgctctgagttggaatctgaggccgga
# ctactcgagggcgggctacagaatgatgtcggtggtggatcccaatctttgtaaacgtgtcgctcttcgccacactgttgggatcacgggactctgtt
# tcctggcccctgtggtcgacctgacctctcctctctttcccgtaatgtctctacctctcaacctctacttcacatatctaggctggaagttttaccaa
# cagggagacagcaattcatctaggaagttgttccgttttagtttattacatataccgttacttattttgcttttaattgtgaacaaacctgaccaaaa
# aaaggcggcaaaacaatcgcaggacactgcggtaaaagtcattcctgaatga]
# protein sequence = [AWIMAAIMFCWQFPHFNALSWNLRPDYSRAGYRMMSVVDPNLCKRVALRHTVGITGLCFLAPVVDLTSPLFPVMSLPL
# NLYFTYLGWKFYQQGDSNSSRKLFRFSLLHIPLLILLLIVNKPDQKKAAKQSQDTAVKVIPE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370B7D.prfl --predictionStart=0  --predictionEnd=25795  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig18924720180911_busco_2432604931_.temp