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>
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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
>
>
>
> ------------------------------------------------------------------------
>
>
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SFAD
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-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
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