Problems with Pfam

James Abbott j.abbott at imperial.ac.uk
Mon Mar 1 09:55:01 EST 2004

Guy Bottu wrote:

> While trying to index under SRS the latest version (12.0) of the Pfam
> databank I had a "malloc" error. It also occurs when I just do "icarus
> pfam.is". Apparently some entries have become too big. The first
> offending entry is GP120 (PF00516). Has anyoane of you met the same
> problem ? Has anyone an idea about how to fix it ?


This kind of error is normally the result of SRS trying too handle too 
much data at once, and can generally be solved by reducing the size of 
data by parallelising the build, or reducing the size of each part 
within an already parallelised library (see section 7.6.3 of the SRS 
Admin guide, page 119). Lion recently released an update pfam.i file 
which (available from http://downloads.lionbio.co.uk/parser/), which 
does just this for pfama. Try upgrading to the latest version of this 
file then try again. If you are still having problems, try reducing the 
partSizeKb parameter of the pfama $Library definition to further reduce 
the quantity of data being handled at once.

Hope that helps,
Dr. James Abbott
Bioinformatics Software Developer, Bioinformatics Support Service
Imperial College, London

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