Problems with Pfam

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2 total messages Started by Guy Bottu Thu, 26 Feb 2004 15:38

#67

Author: Guy Bottu
Date: Thu, 26 Feb 2004 15:38

11 lines
1817 bytes

	Dear colleagues,

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 ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node

Re: Problems with Pfam

#68

Author: James Abbott
Date: Mon, 01 Mar 2004 14:55

27 lines
2688 bytes

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 ?

Guy,

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,
James
-- 
Dr. James Abbott
Bioinformatics Software Developer, Bioinformatics Support Service
Imperial College, London

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