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Article #68Re: Problems with Pfam
From: James Abbott
Date: Mon, 01 Mar 2004 14:55
Date: Mon, 01 Mar 2004 14:55
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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 $Library definition to further reduce the quantity of data being handled at once. Hope that helps, James -- Dr. James Abbott Bioinformatics Software Developer, Bioinformatics Support Service Imperial College, London
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X-Google-Language: ENGLISH,ASCII-7-bit X-Google-Thread: fa6ec,efa50d2d6364406b X-Google-Attributes: gidfa6ec,public X-Google-ArrivalTime: 2004-03-01 06:55:03 PST Path: arc1-ca.pugleaf.net!archiver1.google.com!news2.google.com!news.maxwell.syr.edu!newsswitch.lcs.mit.edu!bloom-beacon.mit.edu!rfcgr.mrc.ac.uk!hgmp.mrc.ac.uk!net.bio.net From: James Abbott <j.abbott@imperial.ac.uk> Newsgroups: bionet.software.srs Subject: Re: Problems with Pfam Date: 1 Mar 2004 14:55:01 -0000 Organization: Imperial College, London, UK Lines: 28 Sender: mod-srs@rfcgr.mrc.ac.uk Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <c1vfo1$i9p$1@jura.cc.ic.ac.uk> References: <c1iqha$mkm$1@snic.vub.ac.be> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Trace: helium.hgmp.mrc.ac.uk 1078152901 7982 193.62.192.80 (1 Mar 2004 14:55:01 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: Mon, 1 Mar 2004 14:55:01 +0000 (UTC) X-Original-To: bionet-software-srs@net.bio.net User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031023 Thunderbird/0.3 X-Accept-Language: en-us, en X-Auth: PGPMoose V1.1 PGP bionet.software.srs iQCVAwUAQENOxKCIqsWvyF5FAQEv3gP/QjiQ85vP1CSStytALCd7UfaVD7dxE+VH By2I0IZrIUEJBiRJ6/Ms1E7TYQel9yNagGyPriSoMPDZfz84TvWLxQHvlaOn6ZQv Uj1FLj3pdIQuYJdS7++nMZM+USnQVGkn8lntrRNfZFi80E+soqRdRm5HbTg5R6ae FPXcWdC/+pw= =mK5t