Problems with Pfam

"benedict arnold JIC benedict.arnold at bbsrc.ac.uk
Tue Mar 9 08:21:14 EST 2004

Hi Guy,

James has probably covered most of the things you can do vis-a-vis the Icarus side of things. 
Depending on what OS you are using you can also change the datasize limit on the machine, on OSF this is a common occurrence where the limits are set to ridiculously small values. We currently have the datasize hard limit set to 4Gb abd Pfam indexes no problems, usually upping the datasize parameter fixes most things.


Ben Arnold
Computational Biology Support Specialist
John Innes Centre
Colney Lane

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 ? 

        Guy Bottu, 
        Belgian EMBnet Node 


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