# 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..93]--> unknown_A (20) <--[0..5]--> unknown_B (9) <--[0..1]--> unknown_C (10) <--[0..2]--> unknown_D (23) <--[0..44]--> unknown_E (21) <--[14..28]--> unknown_G (14) <--[0..14]--> unknown_H (17) <--[0..2]--> unknown_I (70) <--[1..1]--> unknown_J (24) <--[1..3]--> unknown_K (20) <--[0..8]--> unknown_L (25) <--[0..3]--> unknown_M (10) <--[0..56]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3214720180911_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 = 14226, name = Contig32147) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig32147	AUGUSTUS	gene	8448	11056	0.09	+	.	g1
Contig32147	AUGUSTUS	transcript	8448	11056	0.09	+	.	g1.t1
Contig32147	AUGUSTUS	start_codon	8448	8450	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	intron	8506	10548	0.15	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	intron	10782	10867	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	CDS	8448	8505	0.17	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	CDS	10549	10781	0.54	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	CDS	10868	11056	0.88	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32147	AUGUSTUS	stop_codon	11054	11056	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttgaagcagcgatccattgtggtgatgaactttggtttggtgttggtatggaggtgtgaaaatcctgccagagaaa
# gaaaggacataagagctagaaatggcaaggcaggggcagcatacttgcagcagaaaaacatctggtgctccaaggtggtgtcgactctcatgaagatc
# aagttgttcaactccaacggcaagtcattgccactgagtggaacggagacatgggtaacaacaaagaccaccaccaggaaagtgcagactttcatcaa
# cagctgcctgagaagagtgcagaaaatggtgatggattgggcacatacagccaataaatcaccagacagacgatctcatggaattcccagggaaaaca
# gaagagaggtcatccaagaaacctcaggtgatgtgacctggagacaggaggaagatgaggtacacctagaaacaactagagagggcagccaaggactg
# gaggactga]
# protein sequence = [MLKQRSIVVMNFGLVLVWRCENPARERKDIRARNGKAGAAYLQQKNIWCSKVVSTLMKIKLFNSNGKSLPLSGTETWV
# TTKTTTRKVQTFINSCLRRVQKMVMDWAHTANKSPDRRSHGIPRENRREVIQETSGDVTWRQEEDEVHLETTREGSQGLED]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QVI.prfl --predictionStart=0  --predictionEnd=32864  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3214720180911_busco_2432604931_.temp