# 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..352]--> unknown_A (15) <--[1..17]--> unknown_B (21) <--[10..42]--> unknown_D (37) <--[2..11]--> unknown_E (15) <--[2..34]--> unknown_F (17) <--[0..1]--> unknown_G (17) <--[0..6]--> unknown_H (21) <--[0..9]--> unknown_I (34) <--[0..1]--> unknown_J (7) <--[1..6]--> unknown_K (33) <--[24..42]--> unknown_O (11) <--[1..18]--> unknown_P (21) <--[2..15]--> unknown_Q (19) <--[0..11]--> unknown_R (69) <--[4..26]--> unknown_S (32) <--[3..38]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig497420180911_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 = 5492, name = Contig4974) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig4974	AUGUSTUS	gene	325	5492	0.02	-	.	g1
Contig4974	AUGUSTUS	transcript	325	5492	0.02	-	.	g1.t1
Contig4974	AUGUSTUS	stop_codon	325	327	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	575	1900	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	1924	2375	0.29	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	2644	3411	0.63	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	3511	3987	0.62	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	4113	4193	0.45	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	4266	4898	0.23	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	intron	5030	5492	0.78	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	325	574	0.71	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	1901	1923	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	2376	2643	0.45	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	3412	3510	0.64	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	3988	4112	0.93	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	4194	4265	0.45	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4974	AUGUSTUS	CDS	4899	5029	0.26	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [attatgcaggaaagttgtccatcaatcggaaggaaaccaaagggacgatctgtcatatagtcaaacagctacctcaggt
# tagttatatagtcaaagggacaatctgtcatatagtcaaacagctacctcaggtatttcataaactaccggtgtcctcctatgcagaattgccagatg
# tcagattcgactttttcctcaaaaaaattctcccgacacagaaggaccccgtgatgtcacagaccctggtttttatctcgtcttacttcgattacgtc
# agaatacgtaactactttgtacgagaggatatcgagttcgctcaaattaacgagtactcgagcaccaagacaatcacccgatcaagaagtgaattttt
# ccacggccgagttcactttatgttgtacacagagagaattcacttctacaaaagattaaagttgcggggaatccgccacctagtgttttatgaactcc
# gttacccccacttctacagcgagatgtgtaacatgctacaggacagtcgcagacagacggacaaggaaaatatgaccagcaccgtccttattccagct
# tcgatgcccagagactgcggacatcgtgggaacggacagggcagctcgcatgatcacctcaaccaagaaaacccacatgtttgttactggggaaaatt
# cctgagaatggaaacaaaaatatcaaggattcaaggatatgacaggcaattattaaagttgcggggaatccgccacctagtgttttatgaactcccgc
# ggtacccccacttctacagcgagatgtgtaacatgctacaggacagtcgcagacagacggacaaggaaaatatgaccagcaccgtcctttattccagc
# ttcgatgcccagagactggccgacatcgtgggaacggacagggcagctcgcatgatcacctcaaccaagaaagcccacatgtttgttaccggggaaaa
# ttcctga]
# protein sequence = [YAGKLSINRKETKGTICHIVKQLPQVSYIVKGTICHIVKQLPQVFHKLPVSSYAELPDVRFDFFLKKILPTQKDPVMS
# QTLVFISSYFDYVRIRNYFVREDIEFAQINEYSSTKTITRSRSEFFHGRVHFMLYTERIHFYKRLKLRGIRHLVFYELRYPHFYSEMCNMLQDSRRQT
# DKENMTSTVLIPASMPRDCGHRGNGQGSSHDHLNQENPHVCYWGKFLRMETKISRIQGYDRQLLKLRGIRHLVFYELPRYPHFYSEMCNMLQDSRRQT
# DKENMTSTVLYSSFDAQRLADIVGTDRAARMITSTKKAHMFVTGENS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703N5.prfl --predictionStart=0  --predictionEnd=20570  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig497420180911_busco_2432604931_.temp