# 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
# --[10..146]--> unknown_A (15) <--[0..1]--> unknown_B (13) <--[0..20]--> unknown_C (13) <--[0..109]--> unknown_D (18) <--[2..4]--> unknown_E (35) <--[0..4]--> unknown_F (12) <--[0..1]--> unknown_G (18) <--[0..7]--> unknown_H (32) <--[0..1]--> unknown_I (12) <--[5..14]--> unknown_J (25) <--[1..3]--> unknown_K (29) <--[23..47]--> unknown_M (14) <--[1..38]--> unknown_N (13) <--[24..65]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2110020180911_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 = 14770, name = Contig21100) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig21100	AUGUSTUS	gene	1	3407	0.58	-	.	g1
Contig21100	AUGUSTUS	transcript	1	3407	0.58	-	.	g1.t1
Contig21100	AUGUSTUS	intron	1	196	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21100	AUGUSTUS	intron	375	3354	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21100	AUGUSTUS	CDS	197	374	0.96	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig21100	AUGUSTUS	CDS	3355	3407	0.83	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21100	AUGUSTUS	start_codon	3405	3407	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgcactctaatctggtcatcaacctgtgggaagacgttttgagacagaagtcctatgattttcacgacttgtatg
# ttgacggtgcagttcagattgcgaaaatcgccaaggagatgggtgtagagaggttaatccatttttcacacctgaatgcggaccccaagcgcactgat
# ctaatccattttggtgatgatattcctaaaggaaattctatgttacagaaaaag]
# protein sequence = [MMHSNLVINLWEDVLRQKSYDFHDLYVDGAVQIAKIAKEMGVERLIHFSHLNADPKRTDLIHFGDDIPKGNSMLQKK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QBR.prfl --predictionStart=0  --predictionEnd=24784  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2110020180911_busco_2432604931_.temp