makeblastdb check for correct formatting
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5 months ago

hello, I made a blast database with

makeblastdb -in GRCh38.fa -dbtype nucl -out GRCh38.fa


the execution is fine but is there a way to check if the formatting is correct? Thank you

software error blastdb sanity check • 244 views
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out of curiosity : why do you want to check that? do you suspect something not being OK?

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Yes, I am using a program that calls blast internally and I am getting errors such as [main_samview] random alignment retrieval only works for indexed BAM or CRAM files. and FileNotFoundError: [Errno 2] No such file or directory: '/home/gigiux/Documents/Transposons/Results/A0N-vs-Human endogenous retrovirus.bam.9'. I would like to exclude basic mistakes before debugging further...

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the samview error/warning on the retrieval you can resolve by indexing your bam files (this has nothing to do with blast itself though)

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5 months ago
GenoMax 102k

From blast+ package:

   $blastdbcheck -h USAGE blastdbcheck [-h] [-help] [-db DbName] [-dbtype molecule_type] [-dir DirName] [-recursive] [-verbosity DefaultKey] [-full] [-stride StrideLength] [-random NumSequences] [-ends NumSequences] [-no_isam] [-legacy] [-must_have_taxids] [-cdd_delta] [-version] DESCRIPTION BLAST database integrity and validity checking application  ADD COMMENT 0 Entering edit mode I got this: $ blastdbcheck -db ~/Documents/Transposons/GRCh38.fa -dbtype nucl -full
Writing messages to <stdout> at verbosity (Summary)
ISAM testing is ENABLED.
Legacy testing is DISABLED.
TaxID testing is DISABLED.
Using full' mode: every OID will be tested.

Testing 1 volume(s).
/home/gigiux/Documents/Transposons/GRCh38.fa / MetaData:   [ERROR] caught exception.
Result=FAILURE. 1 errors reported in 1 volume(s).
Testing 0 alias(es).
Result=SUCCESS. No errors reported for 0 alias(es).

Total errors: 1
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what is the exact error you're getting from running this?

side note: it's not because this check fails there is for sure something wrong with your blast DBs. (it could for instance complain on missing some of the taxid files, which is not a vital thing for running blasts)

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It is related to absence of taxonomy DB, which may be fine in this case.