[Bioperl-l] Remote Blast error - 500 Too many open files

Stefan Wächter s_waechter at gmx.net
Sun Dec 5 16:39:33 EST 2004

Hi all,

I get the same error like Affan Qureshi a couple of weeks ago.
I wrote a script, that send a couple of hundreds sequences in portions 
of one hundred to NCBI Blast Server using the  RemoteBlast module. After 
a while I the script breaks with an error like that below.
For me it seems that the remote blast module stores the HTML output from 
NCBI in this cryptic filenames in the tmp directory. First the page with 
the RID is stored followed by the complete result page from NCBI . All 
these tmp-files are deleted, when the script is finished. The problem 
seems to be, that these files are accumulated when the script is 
running.  I assume that there is a limit in how many files could be 
stored in a unix/linux directory. Another questions : Why are these 
files still open ? In the moment I havn't found a solution for that 
Did someone know how to manage this problem ?
Is there a possibility to tell the RemoteBlast module to delete these 
tmp files immediately when they are no longer required ?

Thanks for your help

Affan Qureshi wrote:

>I tried a remote blastx search today around 1:00pm and got this error
>message after a long wait. Also it seemed that the NCBI web interface was
>taking too long for BLAST searches.
><HEAD><TITLE>An Error Occurred</TITLE></HEAD>
><H1>An Error Occurred</H1>
>500 Cannot write to '/tmp/hLFqVvHO2D': Too many open files
>Is this a remote server error or am I doing something wrong? Anyone else
>got this error?
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