Error "mdb_env_open: No such file or directory" on trying to execute NCBI psiblast

Question

[Koji]

I am trying to run psiblast with database files downloaded from NCBI site.

I downloaded the latest version of nr.00., nr.01.,... from NCBI site, extract files from all tar.gz files, and put them all in the directory named '/home/kdoi2/raid/nr'.

When I run the test run from the command line as follows, I got the results successfully without error.

$ cd /home/kdoi2/raid/nr
$ ~/raid/ncbi-blast-2.11.0+/bin/psiblast -db nr -query test.fasta

I want psiblast to be able to run in any directory. However, when I try to run it in another directory,

$ cd /home/kdoi2/work
$ ~/raid/ncbi-blast-2.11.0+/bin/psiblast -db nr -query test.fasta  

The process was terminated with following error.

Error: mdb_env_open: No such file or directory

I tried adding the following environment variable settings, but the situation did not improve.

$ BLASTDB=/home/kdoi2/raid/nr  ~/raid/ncbi-blast-2.11.0+/bin/psiblast -db nr -query test.fasta

The contents of nr.pal are as follows.

#
# Alias file created 06/01/2022 05:20:27
#
TITLE All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects
DBLIST nr.00 nr.01 nr.02 nr.03 nr.04 nr.05 nr.06 nr.07 nr.08 nr.09 nr.10 nr.11 nr.12 nr.13 nr.14 nr.15 nr.16 nr.17 nr.18 nr.19 nr.20 nr.21 nr.22 nr.23 nr.24 nr.25 nr.26 nr.27 nr.28 nr.29 nr.30 nr.31 nr.32 nr.33 nr.34 nr.35 nr.36 nr.37 nr.38 nr.39 nr.40 nr.41 nr.42 nr.43 nr.44 nr.45 nr.46 nr.47 nr.48 nr.49 nr.50 nr.51 nr.52 nr.53 nr.54 nr.55 nr.56 nr.57 nr.58 nr.59 
NSEQ 484513096
LENGTH 187235721710

From the manual, it does not appear that there is a problem with the nr.pal file. Also, it is clear from the result shown first that there is no problem with the database file either.

So what is the problem?

[GenoMax]

Did you set the BLASTDB variable on an independent command line? It looks like you are mixing it with an actual command line.

Can you simply try

~/raid/ncbi-blast-2.11.0+/bin/psiblast -db /home/kdoi2/raid/nr/nr -query test.fasta  

and tell us if it works?

[Koji]

Can you simply try ... and tell us if it works?

Unfortunately, the situation has not changed.

$ printenv BLASTDB 
/home/kdoi2/raid/nr
$ ls ${BLASTDB}/nr.pal
/home/kdoi2/raid/nr/nr.pal
$ ~/raid/ncbi-blast-2.11.0+/bin/psiblast -db nr -query test.fasta  
Error: mdb_env_open: No such file or directory
$ ~/raid/ncbi-blast-2.11.0+/bin/psiblast -db /home/kdoi2/raid/nr/nr -query test.fasta
Error: mdb_env_open: No such file or directory

Answer 1

[GenoMax]

Can you run the following?

blastdbcheck -db /home/kdoi2/raid/nr/nr

It should produce something like following

Testing 60 volume(s).
 Result=SUCCESS. No errors reported for 60 volume(s).
Testing 1 alias(es).
 Result=SUCCESS. No errors reported for 1 alias(es).

This will help verify that your database files are intact.

[Koji]

@GenoMax san, thank you for suggestion.

I tried blastdbcheck. It returned the following error.

[ERROR] caught exception in initializing blastdb Result=FAILURE. 1 errors reported in 1 alias(es).

So I checked MD5 against nr.*.tar.gz, and found a mismatch in one of the 60 archive files. I downloaded it again and tried psiblast again, and it succeeded.

Finally, the problem is solved, though I'm still not convinced why the first test worked. It is why I did not check database files first. Did something go wrong and improperly overwrite the archive file in the process...

Regardless, thanks for the useful advice.

[GenoMax]

Only thing I can think of is perhaps in the first round the file that potentially had the problem was not used. But glad to hear that the problem has been solved.