# 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..663]--> unknown_A (19) <--[1..46]--> unknown_B (38) <--[1..9]--> unknown_C (15) <--[0..24]--> unknown_D (11) <--[0..6]--> unknown_E (11) <--[10..17]--> unknown_F (19) <--[8..19]--> unknown_H (20) <--[1..3]--> unknown_I (18) <--[0..1]--> unknown_J (37) <--[15..40]--> unknown_M (13) <--[1..30]--> unknown_N (20) <--[10..39]--> unknown_O (27) <--[2..8]--> unknown_P (11) <--[8..32]--> unknown_Q (37) <--[11..39]--> unknown_S (20) <--[0..2]--> unknown_T (17) <--[0..32]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5116420180911_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 = 14367, name = Contig51164) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig51164	AUGUSTUS	gene	1502	13238	0.12	+	.	g1
Contig51164	AUGUSTUS	transcript	1502	13238	0.12	+	.	g1.t1
Contig51164	AUGUSTUS	start_codon	1502	1504	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	1517	2852	0.77	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	2949	3653	0.78	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	3777	4258	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	4304	4875	0.65	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	4947	5247	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	5275	7396	0.3	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	7524	7652	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	7719	8697	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	8807	9548	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	9569	12635	0.6	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	intron	12682	13107	0.74	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	1502	1516	0.79	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	2853	2948	0.84	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	3654	3776	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	4259	4303	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	4876	4946	0.67	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	5248	5274	0.37	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	7397	7523	0.41	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	7653	7718	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	8698	8806	0.92	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	9549	9568	0.71	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	12636	12681	0.74	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	CDS	13108	13238	0.93	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig51164	AUGUSTUS	stop_codon	13236	13238	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcagacaagctgggccaccctgcagccaaagtggacattctcgaaaaattaccagtgcccttcggactcgtgaggt
# ttggagttgcccccgatcacccagaagtcaagaatgtcattcacactttcaccaccactgccagaaacgagaggtgtacgttcatggggaacgtggaa
# gtcggtaaagacatctctatcgaagatcttcagcgagcctacacagccgtggtactgtcttatggtgctgatgatgacagaacactggccattaaagg
# ggagaatgtctcgaatgtgatttcgggcccgatcgtattgttgttggtttcaatggactgccacaagacagggagctccgatgtgaaatttagacatg
# gagaaaagaggctaacggaactcctgtacaagaccagcatggagccctctaatgcggagacccaggcagccaaagagtgggagcttagatttagactc
# agtcccacagaggtcatcgagagggcaggaaagggagatgatctggtcaacaaatctgcagtatcgaccaatgaaacagaagacattgagtgtggact
# ggttttcagaagtataggatacaagagtgttcctatagatccaggtgtaccgtttgatgagaggaagggcatcattccgaatcagaaaggaagggtcc
# tagataggccaggtctgtactgtagtggatgggtaacagattgtgacattttccctgtaaatgttgcaaaccatggctgtaaacaaattgtgacattt
# tctgattgggacaagattgacgaggaagagataagacgtggaacagtcattggaaaaccgagagagaagattgtggacatctcagaaatgctgaaagt
# cgcacactcctaa]
# protein sequence = [MSDKLGHPAAKVDILEKLPVPFGLVRFGVAPDHPEVKNVIHTFTTTARNERCTFMGNVEVGKDISIEDLQRAYTAVVL
# SYGADDDRTLAIKGENVSNVISGPIVLLLVSMDCHKTGSSDVKFRHGEKRLTELLYKTSMEPSNAETQAAKEWELRFRLSPTEVIERAGKGDDLVNKS
# AVSTNETEDIECGLVFRSIGYKSVPIDPGVPFDERKGIIPNQKGRVLDRPGLYCSGWVTDCDIFPVNVANHGCKQIVTFSDWDKIDEEEIRRGTVIGK
# PREKIVDISEMLKVAHS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DP4.prfl --predictionStart=0  --predictionEnd=22993  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5116420180911_busco_2432604931_.temp