# 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
# --[2..277]--> unknown_A (13) <--[0..1]--> unknown_B (10) <--[0..1]--> unknown_C (33) <--[18..46]--> unknown_E (19) <--[3..18]--> unknown_F (15) <--[0..1]--> unknown_G (18) <--[2..20]--> unknown_H (50) <--[0..3]--> unknown_I (19) <--[17..38]--> unknown_K (17) <--[0..1]--> unknown_L (8) <--[0..5]--> unknown_M (36) <--[10..63]--> unknown_N (19) <--[21..172]--> unknown_P (16) <--[0..15]--> unknown_Q (14) <--[3..8]--> unknown_R (16) <--[3..22]--> unknown_S (46) <--[1..33]--> unknown_T (20) <--[0..2]--> unknown_U (16) <--[2..9]--> unknown_V (31) <--[77..720]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4772320180911_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 = 24594, name = Contig47723) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig47723	AUGUSTUS	gene	13134	24533	0.35	+	.	g1
Contig47723	AUGUSTUS	transcript	13134	24533	0.35	+	.	g1.t1
Contig47723	AUGUSTUS	start_codon	13134	13136	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	13169	17374	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	17477	17921	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	18049	18512	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	18672	19082	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	19250	19815	0.92	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	intron	19991	24404	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	13134	13168	0.56	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	17375	17476	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	17922	18048	0.82	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	18513	18671	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	19083	19249	0.92	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	19816	19990	0.96	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	CDS	24405	24533	0.96	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig47723	AUGUSTUS	stop_codon	24531	24533	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaggacaccgaggtaaaactctttcggatcagagaaaagatggctcaggcatacgattttgctttagacaaaatgg
# ggatggatataatgtcttatcaaatctggctggactatatcaacttcctgaaatcagtagaagctgtgggttcgtatgcagaaaatcaacagataacg
# gctgtgagaaaggtgtttcagagaggtgttgtgaaccctatgataaacatagagggactctggaaggactattgtcagtacgagcagaatataaatcc
# actgattgccaaaaaaatgacggaagaccgaggacgggaatatatcaatgcgagaagggtcgccaaagagtacgaggctgtcacaaggggtctgaaca
# agaaccttccctctgtacccccacagaataacccagacgaggcccagcaggtggatctgtggaaaaaatacatcacatgggagaaaagtaacccccta
# aggacggaagaccacgccctgatcaccaagcgaggtagaccaagatcggccactgtagcggagtgtctgtcagccatgttggaggctgccattaagcg
# gctactgattaatatcaaatagctgagtttatctgcctctgatgatttgtgctcccagtgtttgacctctgtgtctgttcttccagtgatgtttgcct
# atgagcaatgtctgctgtgcctgggacaccatcctgacatttggtatgaagcagcatcttacttggaacagtccagcaaaatcctgtctgaaaaaggg
# gaccagaatgcggggaaaatgtttgcggatgaagccgggtcggtgtatgagcgagccatcaccacactaatgaagaataacatgctggtttactttgc
# atatgcagattttgaagaggtactattttga]
# protein sequence = [MKDTEVKLFRIREKMAQAYDFALDKMGMDIMSYQIWLDYINFLKSVEAVGSYAENQQITAVRKVFQRGVVNPMINIEG
# LWKDYCQYEQNINPLIAKKMTEDRGREYINARRVAKEYEAVTRGLNKNLPSVPPQNNPDEAQQVDLWKKYITWEKSNPLRTEDHALITKRGRPRSATV
# AECLSAMLEAAIKRLLINIKXLSLSASDDLCSQCLTSVSVLPVMFAYEQCLLCLGHHPDIWYEAASYLEQSSKILSEKGDQNAGKMFADEAGSVYERA
# ITTLMKNNMLVYFAYADFEEVLF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370D13.prfl --predictionStart=0  --predictionEnd=40017  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4772320180911_busco_2432604931_.temp