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
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
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
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)
MetaData: [ERROR] caught exception.
See: Blastdbcheck Error and http://seqanswers.com/forums/archive/index.php/t-34826.html
It is related to absence of taxonomy DB, which may be fine in this case.
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version 2.3.6
out of curiosity : why do you want to check that? do you suspect something not being OK?
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.andFileNotFoundError: [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...the samview error/warning on the retrieval you can resolve by indexing your bam files (this has nothing to do with blast itself though)