The output from apt-probset-summarize indicates that the cel file is corrupt. Can you try to download the cel file from BASE and examine the size of the file. You should find the file when you view the details of a rawbioassay.
Can you make windows to refuse to delete the files that are created by the plug-in (the temporary word directory). In this way you can examine the files exported from BASE for apt-probset-summarize. Jari philipp-1.kai...@novartis.com wrote: > Dear Jari, > > indeed I tried to evaluate if the error occurs if doing the same procedure > as BASE calls by "hand". In all attempts I couldn't generate the same > error. I also tried to permit the automatic deletion of files by BASE via > access-policy in Windows to see the log file of apt-probset-summarize. > > The last lines of the log file are: > > 03/04/2009 15:54:00 Wrong number of cells: Expecting: 512656 and > Testscan.CEL has: 0 > 03/04/2009 15:54:00 FATAL ERROR: Different chiptypes or probe counts > found. Only first 10 errors printed, see log for rest. > > Thanks for your support. > > Philipp Kaiser > Novartis Pharma AG, Werk Klybeck > NBx PROCESS DEV. BIOINFORMATIC > CHBS, WKL-681.1.10 > Klybeckstrasse 141 > CH-4057 Basel > Switzerland > Phone: +41 61 6962720 > Fax: +41 61 6963373 > Email : philipp-1.kai...@novartis.com > > > > > Jari Häkkinen <j...@thep.lu.se> > 04.03.2009 15:37 > Please respond to > BASE ML <basedb-users@lists.sourceforge.net> > > > To > BASE ML <basedb-users@lists.sourceforge.net> > cc > > Subject > Re: [base] Affymetrix Power Tools Error > > > > > > > Hi, > > The problem seems to be in the apt-probeset-summarize program as you > point out. Have you tried to run the same analysis outside of BASE? What > is the outcome of that? > > > Cheers, > > Jari > > > philipp-1.kai...@novartis.com wrote: >> Hi, >> >> I am trying to get BASE 2.9.2 working with the APT 0.2 plugin on a >> Testserver. >> Envorinment Condition are as follows: >> Windows XP Prof SP2, Tomcat 6, Affymetrix Powertools Version: >> apt-1.10.1-20081103 >> >> In some cases the Conversion of .CEL files to Probeset Signal worked, > but >> most of the time I get the following error Message: >> >> ----------------------------------------------------------------- >> Name Run plugin: APT Summarize plug-in >> Description >> Priority 5 (1 = highest, 10 = lowest) >> Status Error: Unexpected exit of APT sub-process: >> C:\Program Files\Tomcat >> 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file >> CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program >> Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm >> Exit value: 1. >> Percent complete >> 100% >> >> java.io.IOException: Unexpected exit of APT sub-process: >> C:\Program Files\Tomcat >> 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file >> CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program >> Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm >> Exit value: 1. >> at se.uu.lcb.APT.APTPlugin.runBinary(Unknown Source) >> at se.uu.lcb.APT.AbstractExternalBinaryPlugin.run(Unknown Source) >> at >> > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) >> at >> > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) >> at java.lang.Thread.run(Unknown Source) >> ----------------------------------------------------------------- >> >> As I understand the apt-probeset-summarize.exe just returns an error. Is > >> there a possibility to further identify the problem? >> >> Thanks for your support folks! >> >> Philipp Kaiser >> >> >> >> ------------------------------------------------------------------------ >> >> > ------------------------------------------------------------------------------ >> Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise >> -Strategies to boost innovation and cut costs with open source > participation >> -Receive a $600 discount off the registration fee with the source code: > SFAD >> http://p.sf.net/sfu/XcvMzF8H >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> The BASE general discussion mailing list >> basedb-users@lists.sourceforge.net >> unsubscribe: send a mail with subject "unsubscribe" to >> basedb-users-requ...@lists.sourceforge.net > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, > CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source code: > SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > > > ------------------------------------------------------------------------ > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
