# 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..57]--> unknown_A (16) <--[0..2]--> unknown_B (33) <--[0..2]--> unknown_C (26) <--[0..25]--> unknown_D (10) <--[6..44]--> unknown_E (19) <--[0..4]--> unknown_F (9) <--[32..63]--> unknown_H (23) <--[8..92]--> unknown_I (11) <--[0..1]--> unknown_J (23) <--[0..19]--> unknown_K (35) <--[3..18]--> unknown_L (17) <--[10..19]--> unknown_N (21) <--[1..22]--> unknown_O (24) <--[0..1]--> unknown_P (25) <--[0..2]--> unknown_Q (30) <--[0..43]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig11670220180911_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 = 6944, name = Contig116702) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig116702	AUGUSTUS	gene	1	1923	0.27	-	.	g1
Contig116702	AUGUSTUS	transcript	1	1923	0.27	-	.	g1.t1
Contig116702	AUGUSTUS	intron	1	795	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	intron	900	1213	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	intron	1282	1897	0.55	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	CDS	796	899	0.58	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	CDS	1214	1281	0.7	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	CDS	1898	1923	0.55	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig116702	AUGUSTUS	start_codon	1921	1923	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtttgaattggccgaagatctaggtctggcccttgtgaagtacggagagttcttgtatgacaacctgattctctttt
# ccccatctgttgaaggtgacccaatccgagaactggccactgagtgtggggtggagtttgattatgaaaaaacagctgtaattgatcacctgaacttt
# gacatcaaagaccaaggaaag]
# protein sequence = [MFELAEDLGLALVKYGEFLYDNLILFSPSVEGDPIRELATECGVEFDYEKTAVIDHLNFDIKDQGK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CTU.prfl --predictionStart=0  --predictionEnd=21331  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig11670220180911_busco_2432604931_.temp