Qualscore jar file access error (MinGW trunk build rev 3239)

[tgreco]

I have observed when using Qualscore under the MinGW build (rev 3239)
that running the following command through GUI:
java -jar `qualscore.jar` -c 1.0 -p 0.1 HI257_01.pep.xml
results in the following error message:

Unable to access jarfile `qualscore.jar`

Command FAILED

I retrieved the qualscore SVN prior to building, and did not encounter
any qualscore build errors, and the 'qualscore.jar' file is located in
the tpp-bin directory. I can replicate this with different pep.xml
files as well.
-Todd

[Joshua Tasman]

Hi Todd,

The TPP doesn't install java for you or check that it's installed (at this point).  Can you please see if it's installed on your system, and if so, try the test from the command line?

Thanks,
Josh

[tgreco]

Running java -version from the command, I currently have installed:
java version "1.6.0_05"
Java(TM) SE Runtime Environment (build 1.6.0_05-b13)

Running the command from the prompt results in the same error message.
-Todd

On Jun 2, 6:06 pm, "Joshua Tasman" <jtas...@systemsbiology.org> wrote:
> Hi Todd,
>
> The TPP doesn't install java for you or check that it's installed (at this
> point).  Can you please see if it's installed on your system, and if so, try
> the test from the command line?
>
> Thanks,
> Josh
>

[Joshua Tasman]

Ok, thanks.  Testing svn trunk qualscore I'm getting a different error (related to jfreechart) so I'm thinking that the jar is corrupted.  There's been some recent development here, so I'll ask those who've been involved.

Josh

[Ning Zhang]

If /tpp/bin in your path, java might be able to find the jar. If not as show in your case, you could explicitly set up your classpath variable to point to /tpp/bin/Qualscore.jar if you know how to do set up Environment variable on windows.

--Ning

[Joshua Tasman]

Hi Todd,

The current trunk installer isn't setting the environmental variables that Ning described, so please try that and see if it works.

Josh

[tgreco]

Hi Josh,
I added the jar, C:\Inetpub\tpp-bin\qualscore.jar, to the CLASSPATH.
I no longer get the error, Unable to access jar file, but now receive
this error.

Exception in thread "main" java.lang.NoClassDefFoundError: org/jfree/
data/SeriesDataset
Caused by: java.lang.ClassNotFoundException:
org.jfree.data.SeriesDataset
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClassInternal(Unknown Source)

BTW, I am still using a trunk release from SVN, but now v4.1
JETSTREAM.

-Todd

On Jun 3, 12:14 pm, "Joshua Tasman" <jtas...@systemsbiology.org>

[Ning Zhang]

Make sure you also have jfreechart jar file on your classpath. It is an external java library. I am not sure whether it is distributed with TPP. IF not, you can download it from www.jfree.org.

[Joshua Tasman]

By the way, Todd, please note that trunk is now 4.1 RC, which means that (as always) it's the "bleeding-edge" and not necessarily recommeneded for production use.  For stability I would strongly recommend the official release or the current working release branch, branches/4-0rc, which would contain whatever code would make it into 4.0.1 (then 4.0.2, etc.)

Thanks, as always for the testing and feedback!

-Josh

[tgreco]

Thanks for reminding me Josh. I figured while I had some extra time
at ASMS, I would test out the bleeding-edge leading up to 4.0. I have
now switched back to the final 4.0 version to test out Qualscore. I
added the path to qualscore as well as jfreechart.jar. However that
was not successful. Looking at how qualscore is distributed under the
SVN, I noticed that qualscore.jar is expecting the freechart and
various other jar files to be placed in a "lib" subdirectory. After
copying those jar files into the tpp-bin/lib directory, I was able to
eliminate my NoClassDefFoundError. I then encountered this error:
processing SILAC_150_10ppm.mzXML...error: Parse error occurred - 70
java.lang.ArrayIndexOutOfBoundsException: 70
at org.isb.mzxml.MzXMLParser.convertMassList(MzXMLParser.java:384)
at org.isb.mzxml.MzXMLParser.endElement(MzXMLParser.java:312)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(Unknown Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown
Source)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown
Source)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at org.isb.mzxml.MzXMLParser.getScans(MzXMLParser.java:128)
at org.isb.mzxml.MzXML.rapScans(MzXML.java:132)
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:
91)
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:
71)
at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:
197)
at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041)
Exception in thread "main" java.lang.NullPointerException
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:
93)
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:
71)
at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:
197)
at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041)

I think this was because my mzXML file was compressed with zlib.
Using a non-compressed version eliminated this error, but was replaced
by the Out of Memory error:
processing SILAC_150_10ppm.mzXML... 500 1000Exception in thread
"main" java.lang.OutOfMemoryError: Java heap space
at
org.systemsbiology.qualscore.peakselectors.IsotopePeaks.transformScan(IsotopePeaks.java:
88)
at
org.systemsbiology.qualscore.features.MasterFeatureGenerator.calcFeaturesForSpectrum(MasterFeatureGenerator.java:
122)
at org.systemsbiology.qualscore.commandline.Main
$1.processScan(Main.java:227)
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:
109)
at
org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:
71)
at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:
197)
at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041)

Running qualscore on the command-line with -Xmx500m for example fixed
this error. Not sure if this was specific to my set up, but this
seemed to work for me.
-Todd

On Jun 5, 6:11 pm, "Joshua Tasman" <jtas...@systemsbiology.org> wrote:
> By the way, Todd, please note that trunk is now 4.1 RC, which means that (as
> always) it's the "bleeding-edge" and not necessarily recommeneded for
> production use.  For stability I would strongly recommend the official
> release or the current working release branch, branches/4-0rc, which would
> contain whatever code would make it into 4.0.1 (then 4.0.2, etc.)
>
> Thanks, as always for the testing and feedback!
>
> -Josh
>

[David Shteynberg]

I get the same problem running qualscore on a linux node.

-David

[David Shteynberg]

Upon some further inspection I think the source of the problem maybe the java parser in qualscore not being able to read zlib compressed data in the mzXML doc. Can you please check if you data is compressed and try it on a file without compression?

Thanks,

[tgreco]

Hi David,
Sorry I didn't split my post up more clearly, but the top error
message: Parse error occurred - 70
java.lang.ArrayIndexOutOfBoundsException: 70, was definitely the
result of using a zlib compressed mzXML. When I ran the command w/o
compressed mzXML, the error went away. But then I got a Java out of
memory error instead, which I resolved by running qualscore from the
command-line with additional memory allocation (e.g. -Xmx500m). Just
figured I'd post my findings in case others ran into the same thing.
-Todd

On Jun 9, 1:09 pm, "David Shteynberg" <dshte...@systemsbiology.org>
wrote: