Problems with BLAST db, maybe install issue?
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6.8 years ago
sstevens2 • 0

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!

memory install software-error blast • 3.5k views
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What is the exact blast command you are using and what is the output of:

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

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Entering edit mode

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.

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Entering edit mode
6.8 years ago
satshil.r ▴ 50

vim ~/.bashrc
export BLASTDB="dir_to_blastDB"


Or use any gui based editor

gedit ~/.bashrc
sublime ~/.bashrc