# 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
# --[9..26]--> unknown_A (43) <--[0..1]--> unknown_B (10) <--[0..1]--> unknown_C (30) <--[0..36]--> unknown_D (20) <--[0..1]--> unknown_E (24) <--[0..11]--> unknown_F (61) <--[1..395]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3282220180911_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 = 12346, name = Contig32822) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig32822	AUGUSTUS	gene	1	2557	0.38	-	.	g1
Contig32822	AUGUSTUS	transcript	1	2557	0.38	-	.	g1.t1
Contig32822	AUGUSTUS	intron	1	9	0.73	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	intron	109	589	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	intron	676	1502	0.88	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	intron	1625	2495	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	CDS	10	108	0.72	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	CDS	590	675	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	CDS	1503	1624	0.86	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	CDS	2496	2557	0.65	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig32822	AUGUSTUS	start_codon	2555	2557	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctgcagattcagccagaaaaagacatcgttgtggaatttatcaggaatgaaaatttcaagtatgtcagggcacttg
# gggcattctacatgaggctgacaggaactacattagattgttttaaatatcttgaaccactctactatgattatagaagattgaagctgcagaataga
# gatggaggattccagttggtccacatggatgaattcattgacatcttactgagggatgaacgtgtttgtgacataattcttcccagaatccagaagcg
# acatatcctggaggagaataatcagctggagagcagagttagtgcccttgatgaggacctggaggatatggacacagatgaagaggaagtcatg]
# protein sequence = [MLQIQPEKDIVVEFIRNENFKYVRALGAFYMRLTGTTLDCFKYLEPLYYDYRRLKLQNRDGGFQLVHMDEFIDILLRD
# ERVCDIILPRIQKRHILEENNQLESRVSALDEDLEDMDTDEEEVM]
# end gene g1
###
# start gene g2
Contig32822	AUGUSTUS	gene	3271	11116	0.32	+	.	g2
Contig32822	AUGUSTUS	transcript	3271	11116	0.32	+	.	g2.t1
Contig32822	AUGUSTUS	start_codon	3271	3273	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	3375	4911	0.97	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	5043	5420	0.71	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	5597	6279	0.82	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	6599	7894	0.94	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	8358	8863	0.95	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	9039	9929	0.92	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	10019	10631	0.78	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	10734	10872	0.97	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	intron	11045	11107	0.75	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	3271	3374	0.99	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	4912	5042	0.74	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	5421	5596	0.95	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	6280	6598	0.81	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	7895	8357	0.94	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	8864	9038	0.95	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	9930	10018	0.92	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	10632	10733	0.8	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	10873	11044	0.83	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	CDS	11108	11116	0.77	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig32822	AUGUSTUS	stop_codon	11114	11116	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgacctcgcagcgatattttcctgtgaaaaacgataaaaaatttaaatggattgataatggtattgtgaaagacagac
# gaagacctagtgaaaaacactacagacggtttcagctgaatcagaaacaatatggaataggggactttgtgctgattgcgagcagcaaggatgatttc
# caggaagatcctttggagtcagcatatgttgcccaacttcaagatttgtttgttgatggcgaaggaaatgtggctgaagtagagtggtactggacaca
# aaaagagattttaccatccaagttagagagatgtattaaaacatatggtactccacaatcaaatgaagtgttccttaacagggatagaaatgttccca
# gggaaatagatcctgaaacagtgttgtgcagatgcagtgtaaataggggtcattctgaagataagcaattcaaagagggatcaaaatcatttgtggtt
# agcaagacttttgatgggacaaagttccgagaaatggaagatgtcattgtaaagggccagaataaggagatggtgcacaaaaatcacaatgaattcaa
# agaaaaccaagacacaaggccaaagacaagaaggtcatttggaggagttccgtcacggcagttacaggaaaaaaacagtatgttgaatgtcatccctg
# atgatgaggagggggaggctgagggtttgacgtctgtagtgtcccgagtgaaaaaacaggaagacaggcgcaaatcaactggtcagtgttttggacgg
# cgaataaaggcccaggatgtagcctccatgttaatggacgatgatgacagtgattctatatctgtgatatctactgcatcatctagtgtctctagcgt
# tcacagcaggaagtccacacccctgaagtctatactcactcctcaaaagaaacctggacggaaccatctcagtcgcacagaacctcggcagggaagca
# ggagagtgtcattctctacacaggaaggtagaccttccccaaaatctgctgccaaggcagaaaagaaggtgcaaaaagtcatgacaaaaagaatctcg
# gatagcacggaccaaactcggagaaatgaaactcctggtagtgcagaaaggccagccaggaaaagactgagcagacaattcgaaccctcactgccaga
# cacaccaacatcccgaaatctgaggaaaaaaagcaaggtggtttcctatgatgagaatgtggacttttcaccagtcgggaagaacgaggtttacattc
# catcggacagcgattctgatagtgaccactcagaattctgtggacaaactagaaataaaaagcccaggacagccacacccaggacaaccacgcccagg
# accacaaaacaaaggagaagcagtaattgtgcccaacctaagattcccaaccgctgtgaaccgttaacttcacccaccaatgttttagaagaggcaag
# atccaggttacatgtctctgcggttccagacagtcttccttgtagggagacagaatttgaggatatctataactttgtagagagcaaaatcttggatg
# gaacaggcgggtgcatgtacatttcgggagtccctggaacaggtaaaacagcgactgtccttgaagttatccgggcacttcatcaggctacagaccag
# gaagaattgccaggcttcaagtacatagaggtcaatggaatgaaactgacagagcctcgtcaggcctatgttcaaatgcttaaactcatctga]
# protein sequence = [MTSQRYFPVKNDKKFKWIDNGIVKDRRRPSEKHYRRFQLNQKQYGIGDFVLIASSKDDFQEDPLESAYVAQLQDLFVD
# GEGNVAEVEWYWTQKEILPSKLERCIKTYGTPQSNEVFLNRDRNVPREIDPETVLCRCSVNRGHSEDKQFKEGSKSFVVSKTFDGTKFREMEDVIVKG
# QNKEMVHKNHNEFKENQDTRPKTRRSFGGVPSRQLQEKNSMLNVIPDDEEGEAEGLTSVVSRVKKQEDRRKSTGQCFGRRIKAQDVASMLMDDDDSDS
# ISVISTASSSVSSVHSRKSTPLKSILTPQKKPGRNHLSRTEPRQGSRRVSFSTQEGRPSPKSAAKAEKKVQKVMTKRISDSTDQTRRNETPGSAERPA
# RKRLSRQFEPSLPDTPTSRNLRKKSKVVSYDENVDFSPVGKNEVYIPSDSDSDSDHSEFCGQTRNKKPRTATPRTTTPRTTKQRRSSNCAQPKIPNRC
# EPLTSPTNVLEEARSRLHVSAVPDSLPCRETEFEDIYNFVESKILDGTGGCMYISGVPGTGKTATVLEVIRALHQATDQEELPGFKYIEVNGMKLTEP
# RQAYVQMLKLI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UO4.prfl --predictionStart=0  --predictionEnd=22957  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3282220180911_busco_2432604931_.temp