Question: blastp multiple local databases error
0
gravatar for dp
6 days ago by
dp30
dp30 wrote:

Hi I've come across an error/bug using blastp with multiple local databases. I am blasting against a local copy of nr and an in house database. When I blast against each separately there is no problem, but when I use the option:

-db '/path/to/mydb  /path/to/nr'

I get the following error: BLAST Database error: Error pre-fetching sequence data

Any ideas how to deal with this error?

Thanks!

ADD COMMENTlink modified 4 days ago • written 6 days ago by dp30

You will need to aggregate multiple databases with blastdb_aliastool as described here.

ADD REPLYlink written 6 days ago by genomax80k

Thanks! I will try that now. Do you know why the -db option doesn't work? This section of the user manual says: "BLAST has been able to search multiple databases since 1997. The databases can be listed after the “-db” argument or in an alias file"

ADD REPLYlink written 6 days ago by dp30

Good question.

What blast+ version are you using? Latest version of blast uses v5 format blast indexes. Perhaps you may have to re-index your own database to be v5 format in case you are using fresh nr from NCBI (which is now is v5 format).

ADD REPLYlink modified 6 days ago • written 6 days ago by genomax80k

Thanks! Everything should be v5 - I am using BLAST+ 2.10 and fresh nr. I get the same error using an alias file as you suggested

ADD REPLYlink written 6 days ago by dp30

That error seems to come from NCBI's c++ toolkit. Did you compile your own blast? Do you have the latest c++ toolkit?

ADD REPLYlink written 6 days ago by genomax80k

No - I just downloaded the blast+ v2.10 executables for linux

ADD REPLYlink written 6 days ago by dp30

You may want to send a helpdesk ticket into blast help on this. Could be a bug that you have uncovered.

ADD REPLYlink written 6 days ago by genomax80k

OK good idea. Thanks!

ADD REPLYlink written 5 days ago by dp30
2
gravatar for dp
4 days ago by
dp30
dp30 wrote:

I learned that all dbs must have the same value of use_seqids. Since nr was created using use_seqids, this worked once I re-created my db with it as well.

ADD COMMENTlink written 4 days ago by dp30
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