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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>
> ===============================================
> 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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