# 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..81]--> unknown_A (12) <--[1..20]--> unknown_B (11) <--[0..3]--> unknown_C (29) <--[1..2]--> unknown_D (13) <--[1..5]--> unknown_E (29) <--[0..22]--> unknown_F (25) <--[1..11]--> unknown_G (36) <--[0..23]--> unknown_H (18) <--[2..3]--> unknown_I (9) <--[0..1]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig15004320180911_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 = 5503, name = Contig150043) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig150043	AUGUSTUS	gene	2349	3217	0.44	-	.	g1
Contig150043	AUGUSTUS	transcript	2349	3217	0.44	-	.	g1.t1
Contig150043	AUGUSTUS	stop_codon	2349	2351	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	intron	2509	2653	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	intron	2745	3183	0.57	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	CDS	2349	2508	0.95	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	CDS	2654	2744	0.66	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	CDS	3184	3217	0.48	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig150043	AUGUSTUS	start_codon	3215	3217	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcttgcagctgcgcgggagggcggagtttcatacgtgatgacggatggaggttcacccttgtctgttgcagtcgtct
# gctccagcaatcaaaacagaagtatggaggcccacagctttttaagtaagaggggatacaatgttcgatcgttcggaactggcaatcaagtcaagtta
# ccaggagccacgcttgacaaaccaaatatttatgatttcaacacaacctacgatgaaatgtacagagatttaatgagaaaagaccctgaactgtatcc
# ttcatgttga]
# protein sequence = [MLAAAREGGVSYVMTDGGSPLSVAVVCSSNQNRSMEAHSFLSKRGYNVRSFGTGNQVKLPGATLDKPNIYDFNTTYDE
# MYRDLMRKDPELYPSC]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QKS.prfl --predictionStart=0  --predictionEnd=22567  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig15004320180911_busco_2432604931_.temp