Hi Tomas,
It worked after I executed the script from within MZmine directory.
My batch queue has four steps, raw data import, targeted peak detection,
chromatogram builder, and mass detection. I got this following error while
running the batch script. It looks like it failed after the parsing
finished. Did it get stucked at the second step "peak detection"? Why does
it say it is unsupported Operation exception?
[16:40:37|INFO|BatchModeModule]: Running batch from file
examples/test-batch.xml
[16:40:37|INFO|BatchTask]: Starting a batch of 4 steps
[16:40:37|FINEST|TaskQueue]: Adding task "Opening
file/work/02045/jiao/modules/MZmine-2.10/examples/SKBRcontrol_merge_mzData.xml"
to the task controller queue
[16:40:37|FINEST|WorkerThread]: Starting processing of task: Opening
file/work/02045/jiao/modules/MZmine-2.10/examples/SKBRcontrol_merge_mzData.xml
[16:40:37|INFO|MzDataReadTask]: Started parsing file
/work/02045/jiao/modules/MZmine-2.10/examples/SKBRcontrol_merge_mzData.xml
[16:40:45|FINEST|RawDataFileImpl]: Writing of scans to file
/tmp/mzmine9081179317356835981.scans finished
[16:40:45|INFO|MzDataReadTask]: Finished parsing
/work/02045/jiao/modules/MZmine-2.10/examples/SKBRcontrol_merge_mzData.xml,
parsed 20804 of 20804 scans
[16:40:45|SEVERE|BatchModeModule]: Error while running
batch(java.lang.unsupportedoperationexcept...@net.sf.mzmine.desktop.impl.HeadLessDesktop.getSelectedDataFiles
(HeadLessDesktop.java:99))
java.lang.UnsupportedOperationException
at
net.sf.mzmine.desktop.impl.HeadLessDesktop.getSelectedDataFiles(HeadLessDesktop.java:99)
at
net.sf.mzmine.modules.rawdatamethods.targetedpeakdetection.TargetedPeakDetectionModule.runModule(TargetedPeakDetectionModule.java:54)
at
net.sf.mzmine.modules.batchmode.BatchTask.processQueueStep(BatchTask.java:118)
at net.sf.mzmine.modules.batchmode.BatchTask.run(BatchTask.java:72)
at
net.sf.mzmine.modules.batchmode.BatchModeModule.runBatch(BatchModeModule.java:100)
at net.sf.mzmine.main.MZmineCore.main(MZmineCore.java:225)
On Fri, Feb 15, 2013 at 12:14 AM, Tomas Pluskal <plus...@oist.jp> wrote:
> Hi Dian,
>
> The problem probably is that the startMZmine script changes the current
> working directory to the MZmine directory (in order to access its files in
> conf/, lib/ etc).
> That's why it cannot load your test-batch.xml, because it is located in
> another directory than the rest of MZmine.
> I think your problem can be easily solved by
> a) using the full path to test-batch.xml, e.g. 'startMZmine_Linux.sh
> /home/diaz/test-batch.xml'
> b) starting the stastMZmine script from the same working directory as
> where MZmine is located (e.g. './startMZmine_Linux.sh <file>')
>
> Either one should work.
>
> Cheers,
>
> Tomas
>
>
> On Feb 15, 2013, at 1:23 PM, Dian Jiao <oscarj...@gmail.com> wrote:
>
> Hi Tomas, that is because I have my script in the upper directory. If the
> path for the executable was wrong, it would complain that command not
> found. I run the command in the directory where test-batch.xml is saved.
> Thanks,
>
> Dian
>
> On Thu, Feb 14, 2013 at 10:20 PM, Tomas Pluskal <plus...@oist.jp> wrote:
>
>> Hi Dian,
>>
>> From the output below I see that you did not actually run
>> 'startMZmine_Linux.sh test-batch.xml', but you ran '../startMZmine_Linux.sh
>> test-batch.xml'. That is quite different.
>> Which directory did you run that from (the output of 'pwd')?
>> And in which directory did you place the test-batch.xml?
>>
>> Tomas
>>
>>
>> On Feb 15, 2013, at 7:21 AM, Dian Jiao <oscarj...@gmail.com> wrote:
>>
>> I ran the scripts on both Mac and Linux with the following commands:
>> startMZmine_MacOSX.command test-batch.xml
>> startMZmine_Linux.sh test-batch.xml
>>
>> On both systems, it started to print out some information about loading
>> some modules at first and then quit due to the same error. See the complete
>> output below. If you would like to test with my datafile, I have created a
>> dropbox link for download, (
>> https://www.dropbox.com/s/1hnic70bwfzrnps/SKBRcontrol_merge_mzData.xml)
>> although I don't think the script had begun to read the input before it
>> died.
>>
>> login1$ ../startMZmine_Linux.sh test-batch.xml
>> 2000
>> java version "1.7.0_11"
>> Java(TM) SE Runtime Environment (build 1.7.0_11-b21)
>> Java HotSpot(TM) 64-Bit Server VM (build 23.6-b04, mixed mode)
>> [15:59:48|INFO|MZmineCore]: Starting MZmine 2.10
>> [15:59:48|FINE|TmpFileCleanup]: Checking for old temporary files...
>> [15:59:48|FINE|MZmineCore]: Loading core classes..
>> [15:59:48|FINE|MZmineCore]: Initializing core classes..
>> [15:59:48|FINE|MZmineCore]: Loading modules
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.batchmode.BatchModeModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.filtering.datasetfilters.DataSetFiltersModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.io.xmlexport.XMLExportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.io.xmlimport.XMLImportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.io.sqlexport.SQLExportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeGapFillerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.rawdatamethods.targetedpeakdetection.TargetedPeakDetectionModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.cvplot.CVPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.PCAPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.CDAPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.SammonsPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.clustering.ClusteringModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.custom.CustomDBSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaPredictionModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.fragmentsearch.FragmentSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.complexsearch.ComplexSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.OnlineDBSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.glycerophospholipidsearch.GPLipidSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.tic.TICVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.twod.TwoDVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.threed.ThreeDVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.neutralloss.NeutralLossVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.peaklist.PeakListTableModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.peaklist.export.IsotopePatternExportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.peaklist.export.MSMSExportModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.scatterplot.ScatterPlotVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.histogram.HistogramVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotModule
>> [15:59:49|FINEST|MZmineCore]: Loading module
>> net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeCalculatorModule
>> [15:59:50|FINEST|MZmineConfigurationImpl]: Loading desktop configuration
>> [15:59:50|FINEST|MZmineConfigurationImpl]: Loading modules configuration
>> [15:59:51|INFO|MZmineConfigurationImpl]: Loaded configuration from file
>> conf/config.xml
>> [15:59:51|SEVERE|MZmineCore]: Cannot read batch file test-batch.xml
>>
>> On Wed, Feb 13, 2013 at 2:59 AM, Tomas Pluskal <plus...@oist.jp> wrote:
>>
>>> Hi Dian,
>>>
>>> I generated this batch xml file from GUI (batch mode). The scheme
>>> includes raw data input, peak detection, chromatogram builder, and mass
>>> detection. It was saved as test-batch.xml (attached). However when I run in
>>> command line by "startMZmine_Linux.command test-batch.xml" I got the error
>>> "can't read batch file". Why can't the xml file be recognized?
>>>
>>>
>>> There is no script called "startMZmine_Linux.command". There is
>>> "startMZmine_Linux.sh" and "startMZmine_MacOSX.command". Which one did you
>>> run?
>>>
>>> Actually, your batch file works fine on my computer, so if you want
>>> help, please send us the _exact_ command that you executed and the _exact_
>>> and _complete_ output you got.
>>>
>>>
>>> How does it know which raw data file to read in the first place? Is
>>> the raw data supposed to be merged into the batch xml file or it will point
>>> to the raw data file in the batch xml somewhere?
>>>
>>>
>>> Just open the batch file in any text editor. You will see this:
>>> <parameter name="Raw data file names">
>>>
>>> <file>/Users/oscar/work/mzmine/SKBRcontrol_merge_mzData.xml</file>
>>> </parameter>
>>>
>>> You can change the raw data files by editing the batch in the MZmine
>>> GUI, or directly by editing the XML file contents.
>>>
>>> Best regards,
>>>
>>> Tomas
>>>
>>>
>>> ===============================================
>>> Tomas Pluskal
>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>>> University
>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>>> WWW: https://groups.oist.jp/g0
>>> TEL: +81-98-966-8684
>>> Fax: +81-98-966-2890
>>>
>>>
>>
>> ------------------------------------------------------------------------------
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>> Buy your Sophos next-gen firewall before the end March 2013
>> and get the hardware for free! Learn more.
>>
>> http://p.sf.net/sfu/sophos-d2d-feb_______________________________________________
>> Mzmine-devel mailing list
>> Mzmine-devel@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>
>>
>> ===============================================
>> Tomas Pluskal
>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>> University
>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>> WWW: https://groups.oist.jp/g0
>> TEL: +81-98-966-8684
>> Fax: +81-98-966-2890
>>
>>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
>
> http://p.sf.net/sfu/sophos-d2d-feb_______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
>
> ===============================================
> Tomas Pluskal
> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
> University
> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
> WWW: https://groups.oist.jp/g0
> TEL: +81-98-966-8684
> Fax: +81-98-966-2890
>
>
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