We cannot recreate this problem. We have used the CDF importer on BASE
2.5.0beta and 2.4.5 with no problems. One difference may be that we use
jobagents (i.e., running jobs in a different thread than the core BASE
application) but we did not experience any failures prior to switching
to jobagents.
We even tried to give the jobagent 2GBs of memory to play with without
any problems.
So ... we have no clue on what is going on. Are you able to do anything
with your BASE? You are running a pure non-tampered BASE installed
according to the installation instructions?
Can you please send us the information from the about button,
configuration tab.
Jari
matthew lange wrote:
The cdf file mentioned in my original post is called HG-U133_Plus_2.cdf,
and is downloadable from Affymetrix. It is 97 MB.
Here is the Stack trace provided through the BASE CDF ProbeSet Importer
(not using the custom reporter importer here, just the generic one that
comes with base), accessible from the array design page, as verify
Reporters link.
Thanks a bunch for your help. Let me know if I can be more specific.
Kind Regards,
matthew
java.lang.OutOfMemoryError: Java heap space
at java.lang.String.substring(String.java:1770)
at java.lang.String.subSequence(String.java:1803)
at java.util.regex.Pattern.split(Pattern.java:993)
at java.lang.String.split(String.java:2103)
at java.lang.String.split(String.java:2145)
at affymetrix.gcos.cdf.CDFFileData.readTextProbeSets(Unknown Source)
at affymetrix.gcos.cdf.CDFFileData.readTextFormat(Unknown Source)
at affymetrix.gcos.cdf.CDFFileData.open(Unknown Source)
at affymetrix.gcos.cdf.CDFFileData.read(Unknown Source)
at affymetrix.fusion.cdf.FusionCDFData.read(Unknown Source)
at net.sf.basedb.core.Affymetrix.checkIfReportersExists(Affymetrix.java:416)
at
net.sf.basedb.plugins.CdfFileReporterImporter.importFromCdf(CdfFileReporterImporter.java:460)
at
net.sf.basedb.plugins.CdfFileReporterImporter.run(CdfFileReporterImporter.java:183)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
at java.lang.Thread.run(Thread.java:595)
On Dec 3, 2007 11:02 PM , *Nicklas Nordborg* [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] wrote:
-- Forwarded message --
From: *Nicklas Nordborg* [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
Date: Dec 3, 2007 11:02 PM
Subject: Re: [base] Java memory error
To: BASE ML basedb-users@lists.sourceforge.net
mailto:basedb-users@lists.sourceforge.net
Cc: Joseph Fass [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED], [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
Matthew Lange wrote:
I am using the latest Base, and trying to load an initial data
set. My
initial effort was to modify the reporter importer to load some affy
Why have you modified the reporter importer? What modifications have you
made? The regular reporter importer can import Affymetrix csv files
without problems. The hard part may be to come up with regular
expressions that works. Sample configurations can be downloaded from
http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
probes from a csv file. This worked fine for a small list, but
as the
list approached 500 individuals, I started receiving out of memory
What do you mean with individuals? We regularly test with importing
5+ reporters/probesets. It works fine with 500MB memory with room to
spare.
errors from the Java Heap...and even brought Tomcat to its knees on a
couple of occassions. As a workaround, I uploaded the an 80ish
MB CDF
file from Affy, which contains the array design. This went in fine.
Then I tried to use the feature that allows me to import
reporters from
the CDF file--again Java OOM errors, and tomcat whining.
We use the Affymetrix Fusion SDK for reading CDF files. I don't know
about the memory requirements. I think the binary format uses less
memory since data is read from the file at demand. If the file is in
text format everything is parses and stored in memory. The biggest test
file we have is ~40MB text format. Memory usage stays below 100MB while
parsing that file.
We have given Tomcat 2GB to play with, and this seems like it
should be
more than enough. Are there known issues with this utility that I
should be aware of, or is there a rule-of-thumb to follow when
allocating memory to tomcat, based on the size of files that need
to be
parsed? Or maybe another memory setting somewhere that I must have
overlooked?
Are you really sure that you have given
