# 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..59]--> unknown_A (10) <--[9..41]--> unknown_B (12) <--[1..2]--> unknown_C (16) <--[0..13]--> unknown_D (20) <--[0..1]--> unknown_E (20) <--[0..4]--> unknown_F (22) <--[0..9]--> unknown_G (20) <--[0..2]--> unknown_H (38) <--[0..13]--> unknown_I (28) <--[0..4]--> unknown_J (6) <--[0..3]--> unknown_K (92) <--[0..1]--> unknown_L (25) <--[1..18]--> unknown_M (64) <--[0..1]--> unknown_N (16) <--[4..100]--> unknown_O (21) <--[0..155]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6888720180911_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 = 8362, name = Contig68887) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig68887	AUGUSTUS	gene	1	5895	0.09	-	.	g1
Contig68887	AUGUSTUS	transcript	1	5895	0.09	-	.	g1.t1
Contig68887	AUGUSTUS	intron	1	1972	0.38	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	intron	2045	2263	0.61	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	intron	2323	5002	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	intron	5067	5436	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	intron	5569	5809	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	CDS	1973	2044	0.38	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	CDS	2264	2322	0.62	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	CDS	5003	5066	0.83	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	CDS	5437	5568	0.99	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	CDS	5810	5895	0.33	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68887	AUGUSTUS	start_codon	5893	5895	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcacttacgagagggagaatatgagaaagcgcacaccgatttctttgaggcttttaagaattatgatgaatcaggga
# gtcccaggaggacaacttgcctgaaatacctggtgctcgccaacatgttaatgaagtcaggaatcaatccattcgactctcaagagacaaagccgtac
# aaaaatgacccagaaatcttagcaatgacgaatttagtcagaacacaggtgctgattaagttgatcaagccgtacacaagaatccacatccccttcat
# ttctaaggaactgaatattgacccaacagaagtggaaaatcttctagtttcatgtatccttgacagtgctatacatggccggattgaccaggtgaatc
# aggtgttggaactggaccgagagaacactggaacagccag]
# protein sequence = [MHLREGEYEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQETKPYKNDPEILAMTNLVRTQVLI
# KLIKPYTRIHIPFISKELNIDPTEVENLLVSCILDSAIHGRIDQVNQVLELDRENTGTA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CRF.prfl --predictionStart=0  --predictionEnd=25940  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6888720180911_busco_2432604931_.temp