# 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
# --[7..461]--> unknown_B (10) <--[8..18]--> unknown_D (39) <--[13..28]--> unknown_F (20) <--[0..1]--> unknown_G (23) <--[0..2]--> unknown_H (6) <--[10..19]--> unknown_J (20) <--[0..147]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5443020180911_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 = 6304, name = Contig54430) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig54430	AUGUSTUS	gene	1	4294	0.25	-	.	g1
Contig54430	AUGUSTUS	transcript	1	4294	0.25	-	.	g1.t1
Contig54430	AUGUSTUS	intron	1	449	0.94	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	intron	671	946	0.38	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	intron	1025	3118	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	intron	3203	4291	0.79	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	CDS	450	670	0.43	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	CDS	947	1024	0.41	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	CDS	3119	3202	0.92	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	CDS	4292	4294	0.72	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig54430	AUGUSTUS	start_codon	4292	4294	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgtctggtctggacattaacaaagaacatattttggaaatggcatgtattgttacggatgcagacctgaacattc
# ttgcagagagtccggatatcatcatccatcaaccaaacgcggtgctggataacatggatgagtggtgtacccgacaacatgggaagtcaggtttaaca
# gaagctgtgagaaagagtgatatagatctgaagacggcagaaagcacaatgatgaagttcatagagccacatattgttccatcctcctgccctctggc
# agggaacagtgttcactgtgacaagcagttccttcagaagtacatgccaggtttcatgaaacagctccattatagaatactagatgtcagctcaatca
# aagaactttgcag]
# protein sequence = [MMSGLDINKEHILEMACIVTDADLNILAESPDIIIHQPNAVLDNMDEWCTRQHGKSGLTEAVRKSDIDLKTAESTMMK
# FIEPHIVPSSCPLAGNSVHCDKQFLQKYMPGFMKQLHYRILDVSSIKELC]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937106D.prfl --predictionStart=0  --predictionEnd=20682  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5443020180911_busco_2432604931_.temp