# 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..85]--> unknown_B (43) <--[3..22]--> unknown_C (15) <--[0..1]--> unknown_D (8) <--[0..38]--> unknown_E (36) <--[1..9]--> unknown_F (18) <--[0..2]--> unknown_G (9) <--[0..1]--> unknown_H (32) <--[0..14]--> unknown_I (19) <--[1..17]--> unknown_J (13) <--[0..9]--> unknown_K (13) <--[8..20]--> unknown_M (68) <--[5..30]--> unknown_N (25) <--[6..29]--> unknown_P (34) <--[0..174]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2292920180911_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 = 15671, name = Contig22929) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig22929	AUGUSTUS	gene	1	7468	0.16	+	.	g1
Contig22929	AUGUSTUS	transcript	1	7468	0.16	+	.	g1.t1
Contig22929	AUGUSTUS	intron	183	2823	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	intron	2945	3942	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	intron	4103	5137	0.77	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	intron	5210	6012	0.48	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	intron	6120	7385	0.75	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	1	182	0.74	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	2824	2944	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	3943	4102	0.93	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	5138	5209	0.36	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	6013	6119	0.97	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	CDS	7386	7468	0.89	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22929	AUGUSTUS	stop_codon	7466	7468	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgtcttgtctttcagagttggcctgtgatcctacacagcacgccgatctggcggcggtcatcatgcaggaaggtct
# cgccaacgtctgtctcatcacgccaaacatgaccatagtccgcgcaaaaatagaaacgaacattccacgcaaacgcaaaggaagctgtacccagcatg
# acaaggaccagtttgtgacatacatgatggaccaggctatcaagatggagtacaagatcctcattgacaataaatccaaatttgtgatggttcactcc
# tcctcaggattcaagcattctctaaaagagattttacaagaccccgctgtttcctccaaattatcagacacaaaagcgtcaggagaagtcaaagcttt
# agacgatttttaccaaatgttacagaatgaccccaacagggctttttatgggtatgtagtgaatcatggtcccttcagaatggggtacagggttagac
# atgtcgagaaagctgtggaactccaggcagttgagatattacttatctcagatgaactgttcagagctcaaaatattactcaacgaaagcgatatgta
# aaaattgtggacactgtgaaagagtgcggaggagaggtgaaaattttctccagcatgcatatatcaggagaacagttgggactcctgtcagggatagc
# tgcaattttacgatttcccgttcctgatgacgaagatgaagattctgatgacgattga]
# protein sequence = [VSCLSELACDPTQHADLAAVIMQEGLANVCLITPNMTIVRAKIETNIPRKRKGSCTQHDKDQFVTYMMDQAIKMEYKI
# LIDNKSKFVMVHSSSGFKHSLKEILQDPAVSSKLSDTKASGEVKALDDFYQMLQNDPNRAFYGYVVNHGPFRMGYRVRHVEKAVELQAVEILLISDEL
# FRAQNITQRKRYVKIVDTVKECGGEVKIFSSMHISGEQLGLLSGIAAILRFPVPDDEDEDSDDD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FVX.prfl --predictionStart=0  --predictionEnd=24091  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2292920180911_busco_2432604931_.temp