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eugenemel / maven

Maven GUI: Metabolomics Analysis and Visualization Engine
https://github.com/eugenemel/maven/releases
GNU General Public License v3.0
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Issue with processing M005B dataset #715

Closed ngoccalico closed 5 months ago

ngoccalico commented 7 months ago

I was trying to process M005B dataset, but MAVEN crashed spontaneously, especially every time I clicked into a compound CE(20:5;O) with an error segmentation fault: 11

MainWindow::showPeakInfo(peak)
SpectraWidget::setScan(peak) 
SpectraWidget::setCurrentScan(scan)
Scans=5
Reference
7312581.26844e+061.4561e+061.25043e+06828276
[M+K]+ 1 666.639
[M+Na]+ 1 682.613
[M+NH4]+ 1 687.569
KEY= 66
TableDockWidget::updateTagFilter()
MainWindow::setPeakGroup(PeakGroup) 0x7fcb34e70000
MainWindow::updateGUIWithLastSelectedPeakGroup()
EicWidget::setPeakGroup(PeakGroup* group) group= 0x7fcb34e70000
EicWidget::setPeakGroup() group data:
EicWidget::setPeakGroup() group->meanMz= 704.596
EicWidget::setPeakGroup() group->meanRt= 36.5574
EicWidget::setPeakGroup() (m/z, RT) = [ 704.581 - 704.608 ], [ 35.6936 - 37.1638 ]
EicWidget::setPeakGroup() group->compound= CE(20:5;O)
EicWidget::setPeakGroup() group->adduct= [M+NH4]+
 EicWidget::recompute()
 EicWidget::cleanup()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
 EicWidget::computeEICs()
    computeEICs() pullEics().. msec= 21
EicWidget::groupPeaks()
EICWidget::groupPeaksE(): EIC Range =[ 32.765 - 40.0817 ]: found 10 groups
    groupPeaks().. msec= 23
    computeEICs() Done.
EicWidget::replot(PeakGroup* group) group= 0x7fcb34e70000
EicWidget::findPlotBounds() _minX= 32.7532 minutes, _maxX= 40.1041  minutes
EicWidget::findPlotBounds() _minY= 0 , _maxY= 9.25317e+06
 EicWidget::setupColors()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
EicWidget::replot() group= 0x7fcb34e70000
EicWidget::replot() group->meanMz= 704.596
EicWidget::replot() group->meanRt= 36.5574
EicWidget::replot() group->compound= CE(20:5;O)
EicWidget::replot() group->compound= [M+NH4]+
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fcb34e70000
EicWidget::setSelectedGroup(PeakGroup* group) group type= 0
SampleBarPlotWidget::setPeakGroup() group= 0x7fcb34e70000
SampleBarPlotWidget::setPeakGroup() compound= CE(20:5;O)
BarPlot::setPeakGroup() group= 0x7fcb34e70000
BarPlot::setPeakGroup() group= 0x7fcb34e70000  mean= 1092959.750000 , CoV= 1.175445
BarPlot::setPeakGroup() group= 0x7fcb34e70000 completed
SampleBarPlotWidget::setPeakGroup() group= 0x7fcb34e70000 completed
EicWidget::addIsotopicPlot(PeakGroup* group): group= 0x7fcb34e70000
EicWidget::setSelectedGroup() group data:
EicWidget::setSelectedGroup() group->meanMz= 704.596
EicWidget::setSelectedGroup() group->meanRt= 36.5574
EicWidget::setSelectedGroup() group->compound= CE(20:5;O)
EicWidget::setSelectedGroup() group->adduct= [M+NH4]+
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fcb34e70000 completed
EicWidget::addEICLines()
EicWidget::addEICLines() completed
EicWidget::showAllPeaks()
_alwaysDisplayGroup= 0x7fcb34e70000
EicWidget::showAllPeaks() completed
addMS2Events()  found= 51
SpectraWidget::setScan(scan) 
SpectraWidget::setCurrentScan(scan)
Segmentation fault: 11
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ngoccalico commented 7 months ago

hi Phil, the same error showed up when I processed a M004B dataset on Maven. project X0309-M004B

TableDockWidget::updateTagFilter()
MainWindow::setPeakGroup(PeakGroup) 0x7fde3d990e00
MainWindow::updateGUIWithLastSelectedPeakGroup()
EicWidget::setPeakGroup(PeakGroup* group) group= 0x7fde3d990e00
EicWidget::setPeakGroup() group data:
EicWidget::setPeakGroup() group->meanMz= 841.555
EicWidget::setPeakGroup() group->meanRt= 20.2317
EicWidget::setPeakGroup() (m/z, RT) = [ 841.55 - 841.558 ], [ 19.7453 - 20.633 ]
EicWidget::setPeakGroup() group->compound= HemiBMP(16:0/22:3/2:0)
EicWidget::setPeakGroup() group->adduct= [M-H]-
 EicWidget::recompute()
 EicWidget::cleanup()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
 EicWidget::computeEICs()
    computeEICs() pullEics().. msec= 6
EicWidget::groupPeaks()
EICWidget::groupPeaksE(): EIC Range =[ 17.9779 - 22.3766 ]: found 3 groups
    groupPeaks().. msec= 7
    computeEICs() Done.
EicWidget::replot(PeakGroup* group) group= 0x7fde3d990e00
EicWidget::findPlotBounds() _minX= 17.9701 minutes, _maxX= 22.4082  minutes
EicWidget::findPlotBounds() _minY= 0 , _maxY= 6.8467e+06
 EicWidget::setupColors()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
EicWidget::replot() group= 0x7fde3d990e00
EicWidget::replot() group->meanMz= 841.555
EicWidget::replot() group->meanRt= 20.2317
EicWidget::replot() group->compound= HemiBMP(16:0/22:3/2:0)
EicWidget::replot() group->compound= [M-H]-
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fde3d990e00
EicWidget::setSelectedGroup(PeakGroup* group) group type= 0
SampleBarPlotWidget::setPeakGroup() group= 0x7fde3d990e00
SampleBarPlotWidget::setPeakGroup() compound= HemiBMP(16:0/22:3/2:0)
BarPlot::setPeakGroup() group= 0x7fde3d990e00
BarPlot::setPeakGroup() group= 0x7fde3d990e00  mean= 3803160.250000 , CoV= 0.094925
BarPlot::setPeakGroup() group= 0x7fde3d990e00 completed
SampleBarPlotWidget::setPeakGroup() group= 0x7fde3d990e00 completed
EicWidget::addIsotopicPlot(PeakGroup* group): group= 0x7fde3d990e00
EicWidget::setSelectedGroup() group data:
EicWidget::setSelectedGroup() group->meanMz= 841.555
EicWidget::setSelectedGroup() group->meanRt= 20.2317
EicWidget::setSelectedGroup() group->compound= HemiBMP(16:0/22:3/2:0)
EicWidget::setSelectedGroup() group->adduct= [M-H]-
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fde3d990e00 completed
EicWidget::addEICLines()
EicWidget::addEICLines() completed
EicWidget::showAllPeaks()
_alwaysDisplayGroup= 0x7fde3d990e00
EicWidget::showAllPeaks() completed
addMS2Events()  found= 1
SpectraWidget::setScan(scan) 
SpectraWidget::setCurrentScan(scan)
SpectraWidget::overlayCompound() compound= HemiBMP(16:0/22:3/2:0) # m/z= 17
#obs= 311 #matched= 0
MassCalcWidget::setPeakGroup()
MassCalcWidget::setPeakGroup(): grp->computeFragPattern() minMz= 841.55 , maxMz= 841.558
MainWindow::showPeakInfo(peak)
SpectraWidget::setScan(peak) 
SpectraWidget::setCurrentScan(scan)
Scans=7
Reference
3.17902e+064.99306e+065.26669e+064.28405e+063.27018e+0600
[M+Na-2H]- -1 819.57
[M-H2O-H]- -1 859.564
KEY= 66
TableDockWidget::updateTagFilter()
MainWindow::setPeakGroup(PeakGroup) 0x7fde3dff4e00
MainWindow::updateGUIWithLastSelectedPeakGroup()
EicWidget::setPeakGroup(PeakGroup* group) group= 0x7fde3dff4e00
EicWidget::setPeakGroup() group data:
EicWidget::setPeakGroup() group->meanMz= 879.507
EicWidget::setPeakGroup() group->meanRt= 17.7517
EicWidget::setPeakGroup() (m/z, RT) = [ 879.504 - 879.511 ], [ 17.5888 - 18.3001 ]
EicWidget::setPeakGroup() group->compound= HemiBMP(16:1/22:6/2:0)
EicWidget::setPeakGroup() group->adduct= [M+FA-H]-
 EicWidget::recompute()
 EicWidget::cleanup()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
 EicWidget::computeEICs()
    computeEICs() pullEics().. msec= 7
EicWidget::groupPeaks()
EICWidget::groupPeaksE(): EIC Range =[ 16.1903 - 19.7053 ]: found 3 groups
    groupPeaks().. msec= 7
    computeEICs() Done.
EicWidget::replot(PeakGroup* group) group= 0x7fde3dff4e00
EicWidget::findPlotBounds() _minX= 16.1663 minutes, _maxX= 19.7226  minutes
EicWidget::findPlotBounds() _minY= 0 , _maxY= 1.48739e+08
 EicWidget::setupColors()
 EicWidget::clearPlot()
EicWidget::clearPeakAreas()
 EicWidget::clearEICLines()
EicWidget::replot() group= 0x7fde3dff4e00
EicWidget::replot() group->meanMz= 879.507
EicWidget::replot() group->meanRt= 17.7517
EicWidget::replot() group->compound= HemiBMP(16:1/22:6/2:0)
EicWidget::replot() group->compound= [M+FA-H]-
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fde3dff4e00
EicWidget::setSelectedGroup(PeakGroup* group) group type= 0
SampleBarPlotWidget::setPeakGroup() group= 0x7fde3dff4e00
SampleBarPlotWidget::setPeakGroup() compound= HemiBMP(16:1/22:6/2:0)
BarPlot::setPeakGroup() group= 0x7fde3dff4e00
BarPlot::setPeakGroup() group= 0x7fde3dff4e00  mean= 931370.625000 , CoV= 0.235459
BarPlot::setPeakGroup() group= 0x7fde3dff4e00 completed
SampleBarPlotWidget::setPeakGroup() group= 0x7fde3dff4e00 completed
EicWidget::addIsotopicPlot(PeakGroup* group): group= 0x7fde3dff4e00
EicWidget::setSelectedGroup() group data:
EicWidget::setSelectedGroup() group->meanMz= 879.507
EicWidget::setSelectedGroup() group->meanRt= 17.7517
EicWidget::setSelectedGroup() group->compound= HemiBMP(16:1/22:6/2:0)
EicWidget::setSelectedGroup() group->adduct= [M+FA-H]-
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7fde3dff4e00 completed
EicWidget::addEICLines()
EicWidget::addEICLines() completed
EicWidget::showAllPeaks()
_alwaysDisplayGroup= 0x7fde3dff4e00
EicWidget::showAllPeaks() completed
addMS2Events()  found= 28
SpectraWidget::setScan(scan) 
SpectraWidget::setCurrentScan(scan)
Segmentation fault: 11
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Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
Deleting expired sessions...none found.
PMSeitzer commented 7 months ago

Deposit mzrollDbs / libraries here: https://drive.google.com/drive/folders/1EM8q9Op4W0iyty0aRFkN-70FmnmXNEBr

PMSeitzer commented 7 months ago

Every time clicking on the bad peakgroup (276 in M005B), it crashes:

select * from peakgroups 
inner join peaks on peaks.groupId = peakgroups.groupId
-- where peakgroups.compoundName IS "CE(20:5;O)" ORDER BY groupId, rt
where peakgroups.groupId = 276
PMSeitzer commented 7 months ago

This bug is certainly real, but I couldn't reproduce it on my machine. Delaying this work for now, expecting to have to solve this issue eventually.

ngoccalico commented 6 months ago

MAVEN 2.10.15

Project X0308-M005B, reproduced this error again:

SampleBarPlotWidget::setPeakGroup() group= 0x7f7cd77ff400 completed
EicWidget::addIsotopicPlot(PeakGroup* group): group= 0x7f7cd77ff400
EicWidget::setSelectedGroup() group data:
EicWidget::setSelectedGroup() group->meanMz= 577.519
EicWidget::setSelectedGroup() group->meanRt= 40.1858
EicWidget::setSelectedGroup() group->compound= MG(32:0)
EicWidget::setSelectedGroup() group->adduct= [M+Na]+
EicWidget::setSelectedGroup(PeakGroup* group) group= 0x7f7cd77ff400 completed
EicWidget::addEICLines()
EicWidget::addEICLines() completed
EicWidget::showAllPeaks()
_alwaysDisplayGroup= 0x7f7cd77ff400
EicWidget::showAllPeaks() completed
addMS2Events()  found= 540
SpectraWidget::setScan(scan) 
SpectraWidget::setCurrentScan(scan)
Segmentation fault: 11
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@PMSeitzer