# 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..244]--> unknown_A (26) <--[0..6]--> unknown_B (38) <--[1..8]--> unknown_C (15) <--[15..23]--> unknown_D (39) <--[1..6]--> unknown_E (19) <--[0..1]--> unknown_F (29) <--[6..13]--> unknown_H (27) <--[0..1]--> unknown_I (17) <--[5..13]--> unknown_J (30) <--[0..1]--> unknown_K (28) <--[0..1]--> unknown_L (46) <--[1..23]--> unknown_M (29) <--[1..3]--> unknown_N (12) <--[2..3]--> unknown_O (13) <--[10..15]--> unknown_Q (40) <--[1..6]--> unknown_R (31) <--[7..33]--> unknown_T (18) <--[0..17]--> unknown_U (17) <--[1..2]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig15764020180911_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 = 3430, name = Contig157640) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig157640	AUGUSTUS	gene	1	3430	0.1	+	.	g1
Contig157640	AUGUSTUS	transcript	1	3430	0.1	+	.	g1.t1
Contig157640	AUGUSTUS	intron	1	2302	0.2	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	intron	2375	2485	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	intron	2630	2750	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	intron	2926	3261	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	intron	3320	3430	0.61	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	CDS	2303	2374	0.76	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	CDS	2486	2629	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	CDS	2751	2925	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig157640	AUGUSTUS	CDS	3262	3319	0.6	+	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gataacagtacatacggaggtacattcttgtatcacttagatgagggacccctcgttgttgtgggtattgtggttggac
# tagattataaaaatccttacttgagcccattcagagaatttcagcgattcaagcaccacccctcggttgagccattattccgctcgggtaaaagaatc
# ggctacggtgcaagagcactgaacgaggggggagtgcagtccattccaaaactgactttccctggaggttgtatgataggctgtagtccagggttcat
# gaatgtacccaaaatcaagggtacacacaacgccatgaagagtggccttttggcggcagaatcagtatatgaggttgttagtgatgaggaaaaaattt
# cacagtcaccaaccgcaggtttagaaccagtcaagtatgaagagaggctgaagaacagctggttgtggaaggaatt]
# protein sequence = [DNSTYGGTFLYHLDEGPLVVVGIVVGLDYKNPYLSPFREFQRFKHHPSVEPLFRSGKRIGYGARALNEGGVQSIPKLT
# FPGGCMIGCSPGFMNVPKIKGTHNAMKSGLLAAESVYEVVSDEEKISQSPTAGLEPVKYEERLKNSWLWKE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705VV.prfl --predictionStart=0  --predictionEnd=23428  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig15764020180911_busco_2432604931_.temp