garrettlab-uf / lipidmatch_flow Goto Github PK

Program stops, can't read the mzXML files. See code below. Any idea?
Cheers,
Thomas

Preparing to run C:\Software\LipidMatch_Flow-0.0.2\LipidMatch_Flow\MZmine-2.26\startMZmine_Windows.bat with arguments "C:\LipidMatchFlow_WR\Sputum_OxLipids\Temp_Work\test_BatchMode_5ppm_4Targeted__Pos.xml".
Checking physical memory size...
Found 16289 MB memory, 64-bit system
Java version is 1.8.0_201 (64-Bit)
Java maximum heap size set to 14241 MB

java version "1.8.0_201"Java(TM) SE Runtime Environment (build 1.8.0_201-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode)

[9:40:03|INFO|MZmineCore]: Starting MZmine 2.26
[9:40:03|FINE|TmpFileCleanup]: Checking for old temporary files...
[9:40:03|FINE|MZmineCore]: Loading core classes..
[9:40:03|FINE|MZmineCore]: Initializing core classes..
[9:40:03|FINE|MZmineCore]: Loading modules
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.batchmode.BatchModeModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder.ADAPChromatogramBuilderModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.cropper.CropFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.alignscans.AlignScansModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.scansmoothing.ScanSmoothingModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.metaboanalystexport.MetaboAnalystExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mztabexport.MzTabExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.sqlexport.SQLExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.xmlexport.XMLExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.casmiimport.CasmiImportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mztabimport.MzTabImportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.xmlimport.XMLImportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mspexport.MSPExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mgfexport.MGFExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.GNPSExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.siriusexport.SiriusExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeGapFillerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV1_5.ADAP3DecompositionV1_5Module
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.peakcomparisonrowfilter.PeakComparisonRowFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.peakfilter.PeakFilterModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.cvplot.CVPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.PCAPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.CDAPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.SammonsPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.clustering.ClusteringModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.customdbsearch.CustomDBSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaPredictionModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.fragmentsearch.FragmentSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.complexsearch.ComplexSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.OnlineDBSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.glycerophospholipidsearch.GPLipidSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.formulapredictionpeaklist.FormulaPredictionPeakListModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.ms2search.Ms2SearchModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.tic.TICVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.twod.TwoDVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.threed.ThreeDVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.msms.MsMsVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.neutralloss.NeutralLossVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.PeakListTableModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.export.IsotopePatternExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.export.MSMSExportModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.scatterplot.ScatterPlotVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.histogram.HistogramVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeMassCalculatorModule
[9:40:03|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule
[9:40:03|FINEST|MZmineConfigurationImpl]: Loading desktop configuration
[9:40:03|FINEST|MZmineConfigurationImpl]: Loading modules configuration
[9:40:03|INFO|MZmineConfigurationImpl]: Loaded configuration from file conf\config.xml
[9:40:03|INFO|BatchModeModule]: Running batch from file C:\LipidMatchFlow_WR\Sputum_OxLipids\Temp_Work\test_BatchMode_5ppm_4Targeted__Pos.xml
[9:40:03|INFO|BatchTask]: Starting a batch of 10 steps
[9:40:03|INFO|BatchTask]: Starting step # 1
[9:40:03|SEVERE|HeadLessDesktop]: Cannot read file C:\LipidMatchFlow_WR\Sputum_OxLipids\Temp_Work\190426 SputumQC_OxLip_MS_target_pos.mzXML
[9:40:03|WARNING|RawDataImportModule]: Cannot read file C:\LipidMatchFlow_WR\Sputum_OxLipids\Temp_Work\190426 SputumQC_OxLip_MS_target_pos.mzXML
Press any key to continue . . .

For reducing overhead cost, we acquire data in both polarity modes simultaneously using the Orbitrap instrument. This is applicable for Blank, Target and Sample files. MS/MS runs are acquired for both polarities individually.

I was wondering if it's possible to set the "Scan Polarity" filter from msconvert based on the file name suffixes such as _pos or _Neg?
Even if the runs are acquired in single polarity, this will just enforce the expected polarity and should not break the flow for single polarity acquisition runs.