Body: <p>I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : <a href="https://ftp.ncbi.nlm.nih.gov/blast/db/" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/blast/db/</a>. Files in this database go from <code>ref_prok_rep_genomes.00</code> to <code>ref_prok_rep_genomes.12</code>.</p>
  
  <p>In Linux command line, I was able to launch successfully the bash command  <code>blastn -query (my_query) -db ref_prok_re_.genomes.* -out (my_output)</code> with indexes from <code>00</code> to <code>05</code>, but this does not work from indexes <code>06</code> to <code>12</code> (with the same query and output files). The exact same thing occurs with <code>blastdbcmd -info -db ref_prok_rep_genomes.*</code>.</p>
  
  <p>Each time the error displayed is the same: 
  <code>BLAST Database error: Input db vol does not match lmdb vol</code>.</p>
  
  <p>All the <code>ref_prok_rep_genomes</code> files are in the same folder. I downloaded them using <code>wget</code> and extracted them using <code>tar -zxvf</code>. All <code>ref_prok_rep_genomes.*</code> databases (indexes <code>00</code> to <code>12</code>) have <code>nhr</code>, <code>nin</code>, <code>nnd</code>, <code>nni</code>, <code>nog</code> and <code>nsq</code> files. The folder also contains <code>ref_prok_rep_genomes</code> files (without numbers), with  <code>nal</code>, <code>ndb</code>, <code>nos</code>, <code>not</code>, <code>ntf</code> and <code>nto</code> extensions respectively, as well as <code>taxdb.btd</code> and <code>taxdb.bti</code> files.</p>
  
  <p>Do you guys have an idea of what's going on?</p>
  
  <p>Thank you very much for your time :)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-04T08:36:05.190Z
Comments.Text: 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`
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-06T08:41:37.917Z
Comments.Text: 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```
Comments.UserDisplayName: Olivier Coen
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T12:09:37.767Z
Comments.Text: 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```
Comments.UserDisplayName: Olivier Coen
Tags: <database><blast><bash><phylogenetics><blastn>
Title: Cannot blast against specific NCBI databases
ThreadText: # Cannot blast against specific NCBI databases
  
  (Asked by: username_0 on 2020-04-03)
  
  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 :)
  
  **Tags:** database, blast, bash, phylogenetics, blastn
  
  > **Comments:**
  > **username_1**: 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`  
  > **username_0**: 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```  
  > **username_0**: 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```  
  
  ---
  
  ## 0 answers
  
  