# 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..74]--> unknown_A (14) <--[3..7]--> unknown_B (9) <--[0..1]--> unknown_C (129) <--[2..5]--> unknown_D (54) <--[2..12]--> unknown_E (50) <--[3..12]--> unknown_F (30) <--[4..12]--> unknown_G (32) <--[1..129]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5857720180911_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 = 21330, name = Contig58577) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig58577	AUGUSTUS	gene	1	2474	0.73	+	.	g1
Contig58577	AUGUSTUS	transcript	1	2474	0.73	+	.	g1.t1
Contig58577	AUGUSTUS	intron	1	669	0.76	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig58577	AUGUSTUS	intron	798	2216	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig58577	AUGUSTUS	CDS	670	797	0.87	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig58577	AUGUSTUS	CDS	2217	2474	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig58577	AUGUSTUS	stop_codon	2472	2474	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtcacagagttgaggaaatcccagaggtgccattagtggtcagcgacaaggtcgaggagctgaaaaaaaccaaggaaag
# ctgggcctccttaacgcctgaagagggcttggggagatattgcaaaaagctgtttttggatacgagattaccaccgtttcacctgatccacagtaccc
# accatgcaattgaggcatctgatgagtttccgggattccattgtgaagagcaggagattatcgatgaacatgtggcgagcatgaatgtaaacatccat
# ttctttagacagcttgaatcccacgctctggtaatgggagttcatcgccgggataagggcgcccagggacgctccagcacgtgtttacttgcggaatt
# gattcactgttag]
# protein sequence = [HRVEEIPEVPLVVSDKVEELKKTKESWASLTPEEGLGRYCKKLFLDTRLPPFHLIHSTHHAIEASDEFPGFHCEEQEI
# IDEHVASMNVNIHFFRQLESHALVMGVHRRDKGAQGRSSTCLLAELIHC]
# end gene g1
###
# start gene g2
Contig58577	AUGUSTUS	gene	3157	9167	0.02	+	.	g2
Contig58577	AUGUSTUS	transcript	3157	9167	0.02	+	.	g2.t1
Contig58577	AUGUSTUS	start_codon	3157	3159	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	intron	3334	7728	0.05	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	intron	7859	8056	0.76	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	intron	8214	8324	0.96	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	intron	8409	8613	0.8	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	intron	8777	9104	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	3157	3333	0.37	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	7729	7858	0.92	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	8057	8213	0.8	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	8325	8408	0.96	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	8614	8776	0.83	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	CDS	9105	9167	0.53	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig58577	AUGUSTUS	stop_codon	9165	9167	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggtaaaggccaacgggctacgggcaggcgtttacccgttagctggtggaatgaagccgggtagattaggcccccggg
# gcggcggagcatacagggacccaatccggcggattgttgagccccaactaaagcaccatatctatttacaacaagaagccgtcgttcagctgcgcact
# gtatacaaatccaaacgatttagggctggaaagggtaaaatgaggaacagacgaagaatacagaagaggggcccacttattatatacaattccgataa
# tggcataagcagagctttcagaaatattcctggtatcacactcataaatgtatcccgcctgaaccttctgaagattgctcctggaggacatgttggac
# ggttttgtatctggacagaatctgctttccgtaaattggataaattatatggtacatggaagaaactggccgcagaaaagcaggattacaacttaccg
# aaacccaagatgaccaattcagatttatcaagattattaaagagtgatgaaattcaatctgctttacgtttacccaaaagagataataatagaagaag
# agttcttaagaagaacccattaaagaatcctagggttatgaaccatctgaatccctacagcaaagtaatgaggaaggctgcgcagaatgtggaggcga
# atcgtaaagctgcccgtcaggccaagctggacgctaaacgaggaatcaaggctccagcaaagccagctgccaagaaaccagcaaaagccaaaccagca
# aagaagtaa]
# protein sequence = [MVKANGLRAGVYPLAGGMKPGRLGPRGGGAYRDPIRRIVEPQLKHHIYLQQEAVVQLRTVYKSKRFRAGKGKMRNRRR
# IQKRGPLIIYNSDNGISRAFRNIPGITLINVSRLNLLKIAPGGHVGRFCIWTESAFRKLDKLYGTWKKLAAEKQDYNLPKPKMTNSDLSRLLKSDEIQ
# SALRLPKRDNNRRRVLKKNPLKNPRVMNHLNPYSKVMRKAAQNVEANRKAARQAKLDAKRGIKAPAKPAAKKPAKAKPAKK]
# end gene g2
###
# start gene g3
Contig58577	AUGUSTUS	gene	12075	14177	0.1	+	.	g3
Contig58577	AUGUSTUS	transcript	12075	14177	0.1	+	.	g3.t1
Contig58577	AUGUSTUS	start_codon	12075	12077	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	intron	12126	12978	0.24	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	intron	12993	13930	0.4	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	CDS	12075	12125	0.23	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	CDS	12979	12992	0.66	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	CDS	13931	14177	0.27	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig58577	AUGUSTUS	stop_codon	14175	14177	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgaagttaagcggtgtggtagtagatgttgttgtgatagtgtgggttgagatggctgacatcacactgcctcaacgca
# actggaatttccgtaacataagcactactcccgtatgtctaggttggcatttgttatctccgagcttagcagctcacgcgcgcggtctgacagcggtc
# gagtcaggctatgggaaatctcgcctcactcccttcatggcaaaaaccatgatcctgaatttatctttcctagtcaggaaggaattcctgttatgtgt
# catcggtaagcgcaacttcgactctaccgttcagtag]
# protein sequence = [MKLSGVVVDVVVIVWVEMADITLPQRNWNFRNISTTPVCLGWHLLSPSLAAHARGLTAVESGYGKSRLTPFMAKTMIL
# NLSFLVRKEFLLCVIGKRNFDSTVQ]
# end gene g3
###
# start gene g4
Contig58577	AUGUSTUS	gene	15104	16418	0.24	+	.	g4
Contig58577	AUGUSTUS	transcript	15104	16418	0.24	+	.	g4.t1
Contig58577	AUGUSTUS	start_codon	15104	15106	.	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	intron	15162	15736	0.28	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	intron	15748	16142	0.36	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	CDS	15104	15161	0.36	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	CDS	15737	15747	0.32	+	2	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	CDS	16143	16418	0.6	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig58577	AUGUSTUS	stop_codon	16416	16418	.	+	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgagaccgatctgtgaggtatatggtctcaagtctaggtggcagggcatcaacaagaggattgtaaactctcaaacca
# gtacaaagcaagttccgaggacgcgagtgacgcaggaaaggaagagcaacttaaccggtcctatctaccagcgaaaggtccccagtctaccattcaga
# ctaccgttaccagacactaacggtcactacggttcattcagtcacaatgtagtgagccgtaccagacactacggtcttactacgtattttgaacttcg
# gttttactacggtcattccacgtctggggtcctgagtcactcgtggccgtacccttcagtgacgttgtga]
# protein sequence = [MRPICEVYGLKSRWQGINKRIVNSQTSTKQVPRTRVTQERKSNLTGPIYQRKVPSLPFRLPLPDTNGHYGSFSHNVVS
# RTRHYGLTTYFELRFYYGHSTSGVLSHSWPYPSVTL]
# end gene g4
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FN1.prfl --predictionStart=0  --predictionEnd=28400  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5857720180911_busco_2432604931_.temp