Problems with BLAST db, maybe install issue?

Question

[sstevens2]

Hey all,

I'm having a bit of trouble with BLAST. I've run the same blast commands [literally] thousands of times. I recently had a bad drive and reformatted my ubuntu server, installing 14 server version (where previously I'd had 12). It doesn't seem to matter if it is blastp or blastn I'm running I still get a similar error message (below) or what files I try on.

I've made the db with makeblastdb for all of the files in question before running blast, so those db files do exist. But I still get an error like the following. The blastn message tells a bit more, though I'm not sure what to do about either message since the db files do exist. My best guess is an incompatibility with the Ubuntu 14? Anyone else had this issue? And fixed it? Or know what the problem is?

BLASTP:

BLAST Database error: No alias or index file found for protein database [filename.faa.db] in search path [/home/username/pathtofiles/::]

BLASTN:

BLAST Database error: No alias or index file found for nucleotide database [filename.fna.db] in search path [(unreachable)/path/startingafterhome/::]
BLAST Database error: CSeqDBAtlas::MapMmap: While mapping file [/home/username/path/startingafterhome/filename.fna.db.nin] with 0 bytes allocated, caught exception:
NCBI C++ Exception:
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_80348_130.14.18.6_9008__PrepareRelease_Linux64-Centos_1433254587/c++/compilers/unix/../../src/corelib/ncbifile.cpp", line 5416: Error: ncbi::CMemoryFileMap::CMemoryFileMap() - To be memory mapped the file must exist: /home/username/path/startingafterhome/filename.fna.db.nin

Thanks!

[h.mon]

What is the exact blast command you are using and what is the output of:

ls /home/username/path/startingafterhome/filename.fna.db.nin

[sstevens2]

Thanks for taking a look at this.

Running that ls was exactly what I did when I first saw it too.

So output of:

ls /home/username/path/startingafterhome/filename.fna.db.nin

Was:

/home/username/path/startingafterhome/filename.fna.db.nin

So the files really are in the path where it is looking for them.

Answer 1

[satshil.r]

You have to set your blastDB directory in your path. Add where you saved your blastDBs to your bash profile. (~/.bashrc)

vim ~/.bashrc
#and add the following 
export BLASTDB="dir_to_blastDB"

Or use any gui based editor

gedit ~/.bashrc
sublime ~/.bashrc