blastn error : mdb_env_open: No such file or directory

Question

[Sowmya Pulapet]

Hi, I have two fasta files which converted from sam files. They both are ~1 gb in size and I want to perform blastn keeping one as query and other as subject. I made a blast database from one fasta file using the following command :

> makeblastdb -in Ref.fa -dbtype nucl -input_type fasta -out Ref_db

Following files were created as a result :

1. Ref_db.ndb
2. Ref_db.nhr
3. Ref_db.nin
4. Ref_db.njs
5. Ref_db.not
6. Ref_db.nsq
7. Ref_db.ntf
8. Ref_db.nto

Then I split the query fasta into several chunks of ~130 mb and ran blastn with the command:

blastn -db Ref_db -query  chunk0.fa -out blastout_chunk0.txt 

But it's giving me the following error :

Error : mdb_env_open: No such file or directory

I don't understand what is the problem here. Could someone please help me with this ?

Thank you.

Answer 1

[Sowmya Pulapet]

The issue is solved as I installed blast v2.13 from it's source tar file downloaded from here. The same version present in conda was not creating the db completely.

Answer 2

[Mensur Dlakic]

This usually means that something is wrong with database index files you created. Try this command:

blastdbcheck -db Ref_db

If that reports an error, you will need to recreate database files with makeblastdb. You may need to verify that your collection of FASTA sequences is also in a correct format.

[Sowmya Pulapet]

I tried the above command got this message:

Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. TaxID testing is DISABLED. By default, testing 200 randomly sampled OIDs.

Testing 1 volume(s).   [ERROR] caught exception in /path/to/Ref_db/ 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

How can I find out what is the exact error ?