Masking and Parsing problem in Standalone BLAST 2.7.1?
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Entering edit mode
2.8 years ago

Dear Sir/Ma'am,

I was performing tBLASTn, Query = protein fasta sequence (n=114 ), Subject= Whole genome sequence

In order to do that, I began with the building of a blast database after masking of sequence data using dustmasker and windowmasker

$dustmasker -in XYZ.fna -infmt fasta -parse_seqids -outfmt maskinfo_asn1_bin -out XYZ_dust.asnb
$windowmasker -in XYZ.fna -infmt fasta -mk_counts -parse_seqids -out XYZ_mask.counts -sformat obinary
$windowmasker -in XYZ.fna -infmt fasta -ustat XYZ_mask.counts -outfmt maskinfo_asn1_bin -parse_seqids -out XYZ_mask.asnb

Till now everything was going well but problem stated during makeblastdb

$makeblastdb -in XYZ.fna -dbtype nucl -parse_seqids -mask_data XYZ_dust.asnb, XYZ_mask.asnb -out XYZ_DB

Error: [makeblastdb] No sequences matched any of the masks provided.
Please ensure that the -parse_seqids option is used in the
filtering program as well as makeblastdb.

Without parse_seqids not shown any error, but in this case, it is important to use parse_seqids as after tBLASTn I have to extract subject sequences according to the hit subject coverage for further gene identification.

It will be an immense help to me if I get a few valuable suggestions to solve this problem.

Thank you,

masking parsing blastdbcmd NCBI BLAST makeblastdb • 915 views
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Entering edit mode
8 months ago

Can you try using -mask_data ‘XYZ_dust.asnb,XYZ_mask.asnb’

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