# 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..74]--> unknown_A (14) <--[3..7]--> unknown_B (9) <--[0..1]--> unknown_C (129) <--[2..5]--> unknown_D (54) <--[2..12]--> unknown_E (50) <--[3..12]--> unknown_F (30) <--[4..12]--> unknown_G (32) <--[1..129]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2993420180911_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 = 4515, name = Contig29934) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig29934	AUGUSTUS	gene	1	3290	0.19	+	.	g1
Contig29934	AUGUSTUS	transcript	1	3290	0.19	+	.	g1.t1
Contig29934	AUGUSTUS	intron	1	1011	0.48	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	intron	1181	2737	0.43	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	intron	2984	3210	0.8	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	CDS	1012	1180	0.42	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	CDS	2738	2983	0.4	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	CDS	3211	3290	0.8	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29934	AUGUSTUS	stop_codon	3288	3290	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gcagcaaggccacttattactgtgtatggagataaaggggaaacaacaaagagcaatgtcactttgccagcagtgttcc
# gtgctccaattagaccagacatcgttatctttgtgcattctcagatgagaaaaaactccagacagccctatgctgtcagtgaaaaagcaggacaccag
# acttctgcagaatcctggggaacaggaagagctgtggcccgtattccccgtgttaggggaggaggaactcacagatctggccagggagccttcggaaa
# catgtgccgaggtggtagaatgtttgcccccaccagaacctggaggcgctggcacagaaaaattaatatcaaccagaagagatacgccatctgttctg
# ccattgctgccacaggaatccccgctattgtcatgtctaaagaaaataaagtatttgtaaaactggacagaatcgtcacagaaggtccatctgttaaa
# gatgatatggttaaaggggtctag]
# protein sequence = [AARPLITVYGDKGETTKSNVTLPAVFRAPIRPDIVIFVHSQMRKNSRQPYAVSEKAGHQTSAESWGTGRAVARIPRVR
# GGGTHRSGQGAFGNMCRGGRMFAPTRTWRRWHRKININQKRYAICSAIAATGIPAIVMSKENKVFVKLDRIVTEGPSVKDDMVKGV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FN1.prfl --predictionStart=0  --predictionEnd=22985  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2993420180911_busco_2432604931_.temp