blastp multiple local databases error
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!
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You will need to aggregate multiple databases with
blastdb_aliastoolas described here.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"
Good question.
What
blast+version are you using? Latest version of blast usesv5format blast indexes. Perhaps you may have to re-index your own database to bev5format in case you are using freshnrfrom NCBI (which is now isv5format).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
That error seems to come from NCBI's c++ toolkit. Did you compile your own blast? Do you have the latest c++ toolkit?
No - I just downloaded the blast+ v2.10 executables for linux
You may want to send a helpdesk ticket into blast help on this. Could be a bug that you have uncovered.
OK good idea. Thanks!