Hi Dian,
It seems you found a bug in the targeted peak detection module. This module had
a problem that prevented it from running in the command line mode.
I already fixed the problem and the fix will be included in the next release of
MZmine. Unfortunately, I cannot promise you the release would come anytime soon.
Please try using the chromatogram builder instead. That one surely works in
command line mode.
Tomas
On Feb 19, 2013, at 7:49 AM, Dian Jiao
<oscarj...@gmail.com<mailto:oscarj...@gmail.com>> wrote:
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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<tel:%2B81-98-966-8684>
Fax: +81-98-966-2890<tel:%2B81-98-966-2890>
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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
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