Just out of curiousity, how many fragments are being created for this large database? mpiformatdb simultaneously opens somewhere between 4 and 7 files per fragment.
ok, duh, in your previous e-mail you said --nfrags=16, which means that your SAN is flaky with somewhere between 64 and ~110 open filehandles. yuck.
I remember reading about someone else who implemented an mpiformatdb-like script that works by splitting the FastA's first then feeding each one individually to NCBI formatdb. There's a paper about it here:
http://www.biomedcentral.com/content/pdf/1471-2105-5-171.pdf -Aaron ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
