# 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..44]--> unknown_A (26) <--[0..33]--> unknown_B (33) <--[0..2]--> unknown_C (26) <--[0..4]--> unknown_D (15) <--[0..1]--> unknown_E (12) <--[0..4]--> unknown_F (17) <--[0..42]--> unknown_G (46) <--[0..25]--> unknown_H (21) <--[0..15]--> unknown_I (45) <--[4..122]--> unknown_J (10) <--[0..2]--> unknown_K (26) <--[0..152]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9868920180911_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 = 2005, name = Contig98689) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig98689	AUGUSTUS	gene	1	1895	0.35	+	.	g1
Contig98689	AUGUSTUS	transcript	1	1895	0.35	+	.	g1.t1
Contig98689	AUGUSTUS	intron	1	260	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	intron	448	1139	0.5	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	intron	1299	1866	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	CDS	261	447	0.5	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	CDS	1140	1298	0.75	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	CDS	1867	1895	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig98689	AUGUSTUS	stop_codon	1893	1895	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ggggatgccttgtgtaagaactgcttttacttcgcctttgaggaagaggtccacaaaaccatcacagatgctaatctgt
# ttgtccgaggggagacggttgccatgcggactatctggcaccggagatcgaacctggctgaccgcttcgaccattacctcttgctcactacattcatt
# agttgtatggattccactgtgctggcgtacgttctgaaggttctgaaccagagatacgactacggcgtgaacctggtcctgttgtctgtagacgaggg
# gatcaccggatacagggacgattcattagaggtcagatgtatgtctgtgtgccggtctgatccggtatctaacggtgaagagaaaccagcagcagtat
# ga]
# protein sequence = [GDALCKNCFYFAFEEEVHKTITDANLFVRGETVAMRTIWHRRSNLADRFDHYLLLTTFISCMDSTVLAYVLKVLNQRY
# DYGVNLVLLSVDEGITGYRDDSLEVRCMSVCRSDPVSNGEEKPAAV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370I7R.prfl --predictionStart=0  --predictionEnd=21989  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9868920180911_busco_2432604931_.temp