Blastdb_Aliastool Error

Question

[holyrapan]

Hi everyone,

I would like to build a human+bacteria+archaea subset of the nr database. So what I did is:

1. Get the nr database
2. Get the GI list of human+bacteria+archaea from Entrez Protein database

3. Use this GI list with blastdb_aliastool to build an aliased database of the subset proteins. I used the following command and get the error

   blastdb_aliastool -db nr -gilist sequence_human_bacteria_archaea_26112013.gi -dbtype prot -out human_bacteria_archaea_nov2013 -title "Human plus bacteria and archaea entries"

   Converted 74595073 GIs from sequence_human_bacteria_archaea_26112013.gi to binary format in human_bacteria_archaea_nov2013.p.gil BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing

Does anyone have any idea what the problem is?

Thanks!

[Michael]

What's the output of: blastdbcmd -info -db nr ?

[holyrapan]

I get BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/Users/holy/blastdatabase/db::/Users/holy/blastdatabase/db:]

But I have the nr.pal file there, or does it need something else?

[Michael]

It might be a path problem, try: blastdbcmd -info -db /Users/holy/blastdatabase/nr and blastdbcmd -info -db /Users/holy/blastdatabase/db/nr. Most likely, your setting should be BLASTDB=/Users/holy/blastdatabase/

It might be a blast db download problem, run update_blastdb.pl nr to check if it is up to date and get the database. Extract the tar.gz file it downloads.

Answer 1

[holyrapan]

It's working now. A database volume was missing. Thanks guys for your help!

Answer 2

[5heikki]

Is 74595073 the number of GIs in your file? Does blastdb_aliastool know where your nr is?

[holyrapan]

Yes, 74595073 is the number of GIs in my file. I have this line BLASTDB=/Users/holy/blastdatabase/db in my .ncbirc files and that's where the nr and the GI file are. And I am in this directory when I issue the command.

[5heikki]

Does blastp work against your nr? How did you set it up? Are you sure -title "syntax with quotes" is allowed?