Hi everyone,
I would like to build a human+bacteria+archaea subset of the nr database. So what I did is:
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!
It's working now. A database volume was missing. Thanks guys for your help!
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.
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What's the output of:
blastdbcmd -info -db nr?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?
It might be a path problem, try:
blastdbcmd -info -db /Users/holy/blastdatabase/nrandblastdbcmd -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 nrto check if it is up to date and get the database. Extract the tar.gz file it downloads.