# 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
# --[1..169]--> unknown_A (22) <--[3..37]--> unknown_B (28) <--[0..15]--> unknown_C (42) <--[5..29]--> unknown_D (46) <--[45..108]--> unknown_F (53) <--[0..57]--> unknown_G (39) <--[0..117]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig10564920180911_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 = 4154, name = Contig105649) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig105649	AUGUSTUS	gene	1	3930	0.35	+	.	g1
Contig105649	AUGUSTUS	transcript	1	3930	0.35	+	.	g1.t1
Contig105649	AUGUSTUS	intron	1	2411	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig105649	AUGUSTUS	intron	2594	3864	0.47	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig105649	AUGUSTUS	CDS	2412	2593	0.98	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig105649	AUGUSTUS	CDS	3865	3930	0.67	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig105649	AUGUSTUS	stop_codon	3928	3930	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tggctaagaagaagtctttgtttgacgataaacccgtggagatccaggagctgacctacatcatcaatcaggatataca
# gggtctgaacaaacaaatcgcacaacttcagcaggtggctcggtctcatcctaacgccaggcatgtacagagtcactccaactccgtggtcgtgtcct
# tacagtccaagcttgccaccatgtccaatgatttcaagcaagttctagaagtcagaacagaggttagttaa]
# protein sequence = [AKKKSLFDDKPVEIQELTYIINQDIQGLNKQIAQLQQVARSHPNARHVQSHSNSVVVSLQSKLATMSNDFKQVLEVRT
# EVS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370U71.prfl --predictionStart=0  --predictionEnd=22605  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig10564920180911_busco_2432604931_.temp