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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===============================================
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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and get the hardware for free! Learn more.
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