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
