# 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..42]--> unknown_A (23) <--[0..20]--> unknown_B (6) <--[0..1]--> unknown_C (30) <--[0..1]--> unknown_D (15) <--[0..1]--> unknown_E (38) <--[0..35]--> unknown_F (43) <--[0..45]--> unknown_G (51) <--[0..4]--> unknown_H (22) <--[0..2]--> unknown_I (22) <--[0..34]--> unknown_J (27) <--[1..7]--> unknown_K (13) <--[0..11]--> unknown_L (16) <--[0..2]--> unknown_M (15) <--[0..1]--> unknown_N (28) <--[0..3]--> unknown_O (10) <--[0..4]--> unknown_P (16) <--[0..9]--> unknown_Q (29) <--[0..26]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5691020180911_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 = 13917, name = Contig56910) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig56910	AUGUSTUS	gene	793	3165	0.19	-	.	g1
Contig56910	AUGUSTUS	transcript	793	3165	0.19	-	.	g1.t1
Contig56910	AUGUSTUS	tts	793	793	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	exon	793	1779	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	stop_codon	961	963	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	intron	1780	1895	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	intron	2252	2379	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	intron	2489	3041	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	CDS	961	1779	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	CDS	1896	2251	0.96	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	exon	1896	2251	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	CDS	2380	2488	0.95	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	exon	2380	2488	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	CDS	3042	3098	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	exon	3042	3165	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	start_codon	3096	3098	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56910	AUGUSTUS	tss	3165	3165	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagggaaatcgtacacattcaggctggacagtgcggaaaccagattggtgctaaattctgggaagtcatctctgatg
# aacatggaattgacccaactggcacataccatggtgactctgatctccagttagagagaattaatgtatactacaatgaagccacaggaggcaaatat
# gtaccccgtgcagtcttggttgacttggagccaggtaccatggattccgtcagatccggcccattcggacagatcttcagaccagacaactttgtctt
# tggacagagtggagctggaaacaactgggctaagggacactacacagaaggagctgaacttgtagactctgttcttgatgttgtacgaaaagaggctg
# aaagctgcgattgtcttcagggattccaacttacacactcccttggtggtggtactggttctggtatgggaacactcctcatctccaaaatccgtgaa
# gaatacccagacagaatcatgaacacattctccgttgtaccctcaccaaaagtatcagacacagtcgtagaaccatacaatgccaccctctccgtcca
# ccaacttgttgagaacacagatgagacatactgcattgacaatgaagctctctatgacatctgcttccgtacattgaaactcaccaccccaacatacg
# gtgacttgaaccatcttgtatccgccaccatgtccggtgtcaccacctgcctccgattccctggtcagttgaacgctgatctcaggaaattggccgtc
# aacatggtacccttcccacgtctccacttcttcatgcccggattcgccccactgacctcccgtggtagccagcaatacagagccctcactgttccaga
# gctcacccaacagatgttcgatgccaagaacatgatggctgcctgtgacccacgtcacggacgctacctcaccgttgccgccatgttccgtggccgca
# tgtccatgaaggaggttgatgaacagatgttgaacgtccagaacaagaacagcagctacttcgttgaatggatccccaacaacgtcaagacagccgtc
# tgtgatatcccaccacgtggtctgaagatgtccgccaccttcgtcggaaacagcactgccatccaggagctcttcaagcgtatctccgagcagttcac
# cgctatgttccgtcgtaaggctttcttgcattggtacactggtgagggtatggacgagatggagttcactgaggctgaatccaacatgaacgacttgg
# tgtctgagtaccaacagtaccaggatgccaccgccgaggaggaggctgagttcgatgaagaggagggtgagggtgaagaggcctaa]
# protein sequence = [MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRS
# GPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVS
# DTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLT
# SRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAMFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFVGNST
# AIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEAEFDEEEGEGEEA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ADO.prfl --predictionStart=0  --predictionEnd=22252  --species=fly ./tmp/Contig5691020180911_busco_2432604931_.temp