I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in this database go from ref_prok_rep_genomes.00 to ref_prok_rep_genomes.12.

In Linux command line, I was able to launch successfully the bash command blastn -query (my_query) -db ref_prok_re_.genomes.* -out (my_output) with indexes from 00 to 05, but this does not work from indexes 06 to 12 (with the same query and output files). The exact same thing occurs with blastdbcmd -info -db ref_prok_rep_genomes.*.

Each time the error displayed is the same: BLAST Database error: Input db vol does not match lmdb vol.

All the ref_prok_rep_genomes files are in the same folder. I downloaded them using wget and extracted them using tar -zxvf. All ref_prok_rep_genomes.* databases (indexes 00 to 12) have nhr, nin, nnd, nni, nog and nsq files. The folder also contains ref_prok_rep_genomes files (without numbers), with nal, ndb, nos, not, ntf and nto extensions respectively, as well as taxdb.btd and taxdb.bti files.

Do you guys have an idea of what's going on?

Thank you very much for your time :)

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    $\begingroup$ Did you checked the integrity of the downloaded files? wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/ref_prok_rep_genomes.??.tar.gz.md5 && md5sum -c *md5 $\endgroup$
    – zorbax
    Commented Apr 4, 2020 at 8:36
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    $\begingroup$ I just did. With any of the md5 files, it gave me ref_prok_rep_genomes.00.tar.gz: OK ref_prok_rep_genomes.01.tar.gz: OK ref_prok_rep_genomes.02.tar.gz: OK ref_prok_rep_genomes.03.tar.gz: OK ref_prok_rep_genomes.04.tar.gz: OK ref_prok_rep_genomes.05.tar.gz: OK ref_prok_rep_genomes.06.tar.gz: OK ref_prok_rep_genomes.07.tar.gz: OK ref_prok_rep_genomes.08.tar.gz: OK ref_prok_rep_genomes.09.tar.gz: OK ref_prok_rep_genomes.10.tar.gz: OK ref_prok_rep_genomes.11.tar.gz: OK ref_prok_rep_genomes.12.tar.gz: OK $\endgroup$ Commented Apr 6, 2020 at 8:41
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    $\begingroup$ Actually I understood what happened. NCBI's new version 5 databases use virtual LMDB memory. They give issues with the previous versions of ncbi-blast+. I managed to fix the problem by (1) updating ncbi-blast+ (currently it is the 2.10.0 version), (2) deleting my previous databases, (3) downloading them again using update_blastdb.pl --decompress <database_name> instead of wget $\endgroup$ Commented Apr 8, 2020 at 12:09


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