# 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
# --[8..201]--> unknown_A (16) <--[0..7]--> unknown_B (33) <--[0..3]--> unknown_C (45) <--[0..1]--> unknown_D (15) <--[7..8]--> unknown_F (12) <--[0..1]--> unknown_G (22) <--[3..13]--> unknown_H (38) <--[3..25]--> unknown_I (24) <--[1..5]--> unknown_J (16) <--[9..25]--> unknown_L (29) <--[0..71]--> unknown_M (20) <--[0..1]--> unknown_N (13) <--[12..47]--> unknown_P (23) <--[5..7]--> unknown_Q (21) <--[12..70]--> unknown_T (22) <--[0..160]--> unknown_U (34) <--[0..2]--> unknown_V (8) <--[0..6]--> unknown_W (25) <--[1..3]--> unknown_X (29) <--[0..37]--> unknown_Y (15) <--[9..49]--> unknown_AA (23) <--[3..25]--> unknown_AB (10) <--[4..6]--> unknown_AC (12) <--[37..595]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig707220180911_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 = 3551, name = Contig7072) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig7072	AUGUSTUS	gene	1	3472	0.36	+	.	g1
Contig7072	AUGUSTUS	transcript	1	3472	0.36	+	.	g1.t1
Contig7072	AUGUSTUS	intron	1	1745	0.7	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	intron	1890	2402	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	intron	2546	3357	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	CDS	1746	1889	0.94	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	CDS	2403	2545	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	CDS	3358	3472	0.58	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig7072	AUGUSTUS	stop_codon	3470	3472	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tatgggccgtccaatcaaagacaattaaaagaggcgtgtcttgttgttgatgtactggattccaaagtaaaaaaggatc
# tcctcacatggtttgtgaaacttcagttatctgagtatctggtcctgtttggtgaaaaagaagaagttgcttggctggacaaaatagacagacgatat
# gcctggataaagcggacgttagtggactttgaagaaaagtttggtcccctgttccccgaagtttgggaggtgtcagaacgaatctgcatagagttctg
# taacataacaagcccccagaccaagtcattaaatccgtttgaagcgtctacaaatccgtttgagacagaatccgatggtgaaatgagtacctctgaag
# aaacaaaggtaacatttagtgccttttaa]
# protein sequence = [YGPSNQRQLKEACLVVDVLDSKVKKDLLTWFVKLQLSEYLVLFGEKEEVAWLDKIDRRYAWIKRTLVDFEEKFGPLFP
# EVWEVSERICIEFCNITSPQTKSLNPFEASTNPFETESDGEMSTSEETKVTFSAF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937092W.prfl --predictionStart=0  --predictionEnd=22804  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig707220180911_busco_2432604931_.temp