# 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..53]--> unknown_A (44) <--[4..5]--> unknown_B (12) <--[5..8]--> unknown_C (49) <--[11..22]--> unknown_D (14) <--[4..25]--> unknown_E (18) <--[1..3]--> unknown_F (17) <--[1..59]--> unknown_G (9) <--[6..23]--> unknown_H (40) <--[2..12]--> unknown_I (8) <--[0..1]--> unknown_J (18) <--[20..81]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig19710920180911_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 = 4691, name = Contig197109) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig197109	AUGUSTUS	gene	1	4460	0.3	+	.	g1
Contig197109	AUGUSTUS	transcript	1	4460	0.3	+	.	g1.t1
Contig197109	AUGUSTUS	intron	1	1947	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	intron	2085	3024	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	intron	3102	3650	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	intron	3751	4416	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	CDS	1948	2084	0.65	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	CDS	3025	3101	0.98	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	CDS	3651	3750	0.86	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	CDS	4417	4460	0.63	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig197109	AUGUSTUS	stop_codon	4458	4460	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aaaacccaagacgcagcagggtaaacgcttcctggagaaacgggagcccaaactgaccgagaatgacaaacaggccatg
# tttatcaagggaggaaacaccagtgttatggtatcacaggtgctgagagaactggtaggtcggttctttgattttcacattttggacatgatagaact
# tggaatggagaagtttgtgtcaatggctgactttcatggagtgaaatgtccagagggtacaaagccgtgtttaatgtttgctggtgagacattcaaac
# aagacatagaatatcagagactgaaaaatttattcattgatcacatggacaagggtcagtctaggtctgtagaccagttttga]
# protein sequence = [KPKTQQGKRFLEKREPKLTENDKQAMFIKGGNTSVMVSQVLRELVGRFFDFHILDMIELGMEKFVSMADFHGVKCPEG
# TKPCLMFAGETFKQDIEYQRLKNLFIDHMDKGQSRSVDQF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370NBT.prfl --predictionStart=0  --predictionEnd=22877  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig19710920180911_busco_2432604931_.temp