This is a test version of Biostars. For the public version, visit https://www.biostars.org.
makeblastdb check for correct formatting

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
• 2,939 views • link
updated by GenoMax 16K • | written by marongiu.luigi 79

out of curiosity : why do you want to check that? do you suspect something not being OK?

• 0 views • link
written by lieven.sterck 1.6K

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...

• 0 views • link
written by marongiu.luigi 79

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

• 0 views • link
written by lieven.sterck 1.6K

1 answer

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
• 0 views • link
written by GenoMax 16K

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
• 0 views • link
written by marongiu.luigi 79

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)

• 0 views • link
written by lieven.sterck 1.6K

Log in to answer this question.

More posts like this
  • makeblastdb Bus error
    written by 860101959 1
    Problem: ``` $makeblastdb -in $reference -parse_seqids -title "hg19" -dbtype nucl Building a new DB, current time: 08/16/2021 14:21:54 New DB name: New DB title: hg19 …
  • Local blast with multiple databases and multiple files
    written by akang 12
    I am trying to run a specific query against specific custom database in python. When i just use one database it works fine but doesnt …
  • makeblastdb undocumented exit code
    written by mpaco 0
    Hello, I am relatively new to blast (version 2.10.0+) on Windows 10, so please bare with me. I tried to make a blast database with …
  • how to makeblastdb with taxon id's
    written by gb 221
    Dear all, I extracted a subset of sequences from the nt database and I want to make a blast database with those sequences including the …
  • local blast on ubuntu 17.04 using refseq_genomic
    written by jf 0
    Hello I am trying to run local blast on ubuntu 17.04. I have blast installed: ncbi-blast+ is already the newest version (2.6.0-1). then export BLASTDB=path/to/blastdb/folder …
  • makeblastdb command not found
    written by linhuixinnn 0
    Hi, I am new to this whole command line Blast+ Suite. Sorry for sounding dumb but I couldnt find useful help sheet online. I am …
  • Error while makeblastdb
    written by sp 2
    I downloaded human chromosome from UCSC and tried to make a "blastable" database. Each chromosomes was saved separately, something like chr1.fa, chr2.fa etc. I would …
  • Local Blast Database
    written by Nano 2
    <p>I need to blast one protein query file against 150 nucleotide files. at first I tried Blast but it says there is not database, I …
  • Why does makeblastdb raise this exception on linux?
    written by ronaldnieuwenhuis 3
    Hello, I am trying to make a blast database of several fasta files. When I use makeblastdb (on linux) however, I am getting an exception …
  • How to create 10GB blast database
    written by arronar 29
    Hello. I want to create a database for local blast but fasta file with reads is 9Gb. So I want from this file to create …