# 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..152]--> unknown_A (22) <--[1..2]--> unknown_B (17) <--[2..4]--> unknown_C (18) <--[0..11]--> unknown_D (14) <--[1..4]--> unknown_E (55) <--[0..1]--> unknown_F (27) <--[0..1]--> unknown_G (13) <--[2..36]--> unknown_H (43) <--[0..71]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2206420180911_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 = 20576, name = Contig22064) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig22064	AUGUSTUS	gene	10055	23378	0.03	-	.	g1
Contig22064	AUGUSTUS	transcript	10055	23378	0.03	-	.	g1.t1
Contig22064	AUGUSTUS	intron	10055	11551	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	11666	12661	0.59	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	12903	14826	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	14865	15349	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	15490	15638	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	15789	16084	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	16258	16379	0.88	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	16573	17864	0.55	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	17984	22919	0.78	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	22995	23056	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	intron	23071	23249	0.72	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	11552	11665	0.73	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	12662	12902	0.6	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	14827	14864	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	15350	15489	0.94	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	15639	15788	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	16085	16257	0.88	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	16380	16572	0.88	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	17865	17983	0.56	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	22920	22994	0.7	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	23057	23070	0.72	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	CDS	23250	23378	0.54	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig22064	AUGUSTUS	start_codon	23376	23378	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgataactatgtccggaagggatcatccacagcagtaccgccctctgttagaggaagaggaggagttcatcagctatg
# atgacaaggactttgaacaacattatgtgagaaagaagaaaatgaggcaactattattaccgtattctggaactaaacttggaaaattcaaaaaagca
# gccatagcatcagatagcaaagtgtgctcggatattggcaataagagtggaacagcctcggtgataaatgcgagagaatctgcacctttgaagtccac
# tgagactatgtatgaaaaggttcacaattcatcagaatatggtaggttaagtggattatattgtggacttagtatagcagttcccggagaaatcaagg
# gatacatggaggcatggaataaatggggcaagttaccgtggaaggatttgtttacagaaagtattgaattagctaaaaatgggtttccaatctccaaa
# catctggcagaaaagatggaatctgcagaaaaagttctcagactggatgaagacacatggaaacactattcaaatccccaaactaaaaaaatgttgaa
# agagggagacataattaaatttccagaattggcagaaacttacaagaaattggcagaaaatggtggtcaggccttttacaatgtaacagagggaagtc
# taggatatgatattatacaagatctcaaagaaaagaaatctataataagtgaagaagaccttacacagtacaccgcagaagtagaagaaccactgaaa
# gtaacgctgagggacggcagtgtcctgtacagccccagaccaccgtccagtggagctgtgctctccttcatacttaatatattagacggttataagat
# gaccactgaaagtcttaaaaccaaagagtcacgtcttactgcttatcatagaatgattgaggcttttaaatttgcatatgctcaaagatcggagcttg
# gagatccagcatttgtttcaaatgtcacagaggtgaaagtcctgccaagggcaataagaatctgggttatatttggttcaggtgtgacaggaaaacga
# acaggaatactgtttaatgatgaaatggatgacttctcttcccctaacatcaccaatgcttttggtatccctccttctccatcgaacttcatcaaacc
# tgggaagcggccattgtcatccatgtgcccagctgtcctagctgataagacaaagaaagtaaagatggtggtgggggccgcgggtggatccaggatta
# caacaaccacagcatatatagccgctcatgttttgtggtttggatacaatataaaagaagcagttgatgccagaagattgcaccatcaactcattcca
# caaataacttatcatgaaccagaatttccaaag]
# protein sequence = [MITMSGRDHPQQYRPLLEEEEEFISYDDKDFEQHYVRKKKMRQLLLPYSGTKLGKFKKAAIASDSKVCSDIGNKSGTA
# SVINARESAPLKSTETMYEKVHNSSEYGRLSGLYCGLSIAVPGEIKGYMEAWNKWGKLPWKDLFTESIELAKNGFPISKHLAEKMESAEKVLRLDEDT
# WKHYSNPQTKKMLKEGDIIKFPELAETYKKLAENGGQAFYNVTEGSLGYDIIQDLKEKKSIISEEDLTQYTAEVEEPLKVTLRDGSVLYSPRPPSSGA
# VLSFILNILDGYKMTTESLKTKESRLTAYHRMIEAFKFAYAQRSELGDPAFVSNVTEVKVLPRAIRIWVIFGSGVTGKRTGILFNDEMDDFSSPNITN
# AFGIPPSPSNFIKPGKRPLSSMCPAVLADKTKKVKMVVGAAGGSRITTTTAYIAAHVLWFGYNIKEAVDARRLHHQLIPQITYHEPEFPK]
# end gene g1
###
# start gene g2
Contig22064	AUGUSTUS	gene	25390	30630	0.05	+	.	g2
Contig22064	AUGUSTUS	transcript	25390	30630	0.05	+	.	g2.t1
Contig22064	AUGUSTUS	start_codon	25390	25392	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	25429	26186	0.29	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	26225	28946	0.13	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	29096	29278	0.47	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	29376	30053	0.52	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	30157	30261	0.6	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	intron	30486	30630	0.78	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	25390	25428	0.3	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	26187	26224	0.3	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	28947	29095	0.14	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	29279	29375	0.37	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	30054	30156	0.58	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig22064	AUGUSTUS	CDS	30262	30485	0.51	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggctgaatcagcacttacagcagcatataagggccttttcgctcagattgtgtcaaaaccctgtggtttgagcagaa
# tgtatgtagatgggaatggtcaactgagagagcgactgctgggatatgatgatctgtacccaggccacataccaacatccaccttacagaaagtgctg
# ctctctgttggctcagcagggatggcgattctggatccaagcagagacgacatgatcgcaacccttggtgagactacaggatcttgggcacttcgttc
# catcaagcagaaaatggaggctgatccaactggacaaaggattcttcaggaacaaccagtcattaatacaagttcagtgtctattgactatctgggaa
# gtttgcctgagggtacatttggaaagaaatactggcatttcctcaacaaaaatggattttctccagatgctagactgccaattcattttgtggatgac
# ccagagttaaagtatgtcatgttgagataccgtcaagtccacgacctttttcactccattcttgggatgccacctcacatgttaggagaggttgctgt
# taagtgggtggaggctctgcagaccgggcttcccatgtgtgctctcggagctttgtttggtccactcagattgggtccaaa]
# protein sequence = [MAESALTAAYKGLFAQIVSKPCGLSRMYVDGNGQLRERLLGYDDLYPGHIPTSTLQKVLLSVGSAGMAILDPSRDDMI
# ATLGETTGSWALRSIKQKMEADPTGQRILQEQPVINTSSVSIDYLGSLPEGTFGKKYWHFLNKNGFSPDARLPIHFVDDPELKYVMLRYRQVHDLFHS
# ILGMPPHMLGEVAVKWVEALQTGLPMCALGALFGPLRLGP]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OO3.prfl --predictionStart=10055  --predictionEnd=50492  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2206420180911_busco_2432604931_.temp