# 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
# --[17..310]--> unknown_A (14) <--[1..5]--> unknown_B (19) <--[4..8]--> unknown_C (14) <--[2..5]--> unknown_D (10) <--[0..2]--> unknown_E (14) <--[0..18]--> unknown_F (32) <--[0..1]--> unknown_G (31) <--[1..2]--> unknown_H (24) <--[10..28]--> unknown_J (23) <--[0..1]--> unknown_K (20) <--[13..64]--> unknown_L (72) <--[8..21]--> unknown_N (16) <--[14..83]--> unknown_P (18) <--[51..202]--> unknown_S (16) <--[18..49]--> unknown_V (12) <--[0..89]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig48970120180911_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 = 5858, name = Contig489701) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig489701	AUGUSTUS	gene	1	4239	0.08	+	.	g1
Contig489701	AUGUSTUS	transcript	1	4239	0.08	+	.	g1.t1
Contig489701	AUGUSTUS	intron	1	680	0.49	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	intron	756	926	0.3	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	intron	971	2273	0.34	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	intron	2280	2388	0.59	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	intron	2536	2764	0.55	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	intron	2869	4148	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	681	755	0.25	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	927	970	0.64	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	2274	2279	0.59	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	2389	2535	0.55	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	2765	2868	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	CDS	4149	4239	0.87	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig489701	AUGUSTUS	stop_codon	4237	4239	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ctcaagaagtaatagagaatggagtgatcaacaagttttttcatggcagtaatccggaagctggtcaggcacacctaca
# tgggggtcagggcacaccagtgagtgggttttggtttaatgaacaggaagccagtgaagttgtcgagttggcctacaacgattacgctaatgccagtc
# agagactgtttctcctggaggaattttatggcccaagttttacgttttttaaggtagtgtgtgtgtgtaatttccccgtgtttctgtgtactaagacc
# ccagacatccgttcattagaccagctactactggtgcaacccgacaaaaaagacatgatcctcagcaacatgaaggatgccctactaacactgataga
# taatatcatcatggcaaccaaagaggccaatggccacatcgctcacctgagcacggcttgcttcactaagaagagcagtagtttgcggatttag]
# protein sequence = [QEVIENGVINKFFHGSNPEAGQAHLHGGQGTPVSGFWFNEQEASEVVELAYNDYANASQRLFLLEEFYGPSFTFFKVV
# CVCNFPVFLCTKTPDIRSLDQLLLVQPDKKDMILSNMKDALLTLIDNIIMATKEANGHIAHLSTACFTKKSSSLRI]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DTG.prfl --predictionStart=0  --predictionEnd=23834  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig48970120180911_busco_2432604931_.temp