search

kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
64 stars 19 forks source link

Can't parse my Raw File #46

Open ncarrut opened 5 years ago

ncarrut commented 5 years ago

Describe the bug rawTools failse to parse my QC run. May be the same issue as: https://github.com/kevinkovalchik/RawTools/issues/2

Description of raw file 100 MB raw file from a 25 minute run. It's a yeast digest with Pierce RT peptides spiked in. Analysis is mixed DDA and targeted for the RT peptides.

Command line arguments RawTools.exe -f Yeast_20181109170737.raw -x

Command line output Please paste the entire output from the command line, if applicable (i.e. everything that appeared after you hit enter until things stopped working).

        Scan: 20738, MSOrder: Ms2
        Scan: 20739, MSOrder: Ms2
        Scan: 20740, MSOrder: Ms2
        Scan: 20741, MSOrder: Ms2
        Scan: 20742, MSOrder: Ms2
        Scan: 20743, MSOrder: Ms2
        Scan: 20744, MSOrder: Ms2

The above scans will not be present in the output data. You should
manually check them to ensure they are not critical to you analysis.

All scans accounted for!
======================================================

Extracting reaction events: 100%

Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at RawTools.Algorithms.ExtractData.Extract.MethodData(IRawDataPlus rawFile, ScanIndex index) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Algorithms\Extraction\ExtractData.cs:line 763
   at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\WorkFlows\DDA.cs:line 80
   at RawTools.Program.Run(Dictionary`2 opts) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Program.cs:line 221
   at RawTools.Program.Main(String[] args) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Program.cs:line 73

Desktop & RawTools information:

Additional context Add any other context about the problem here.

armadillocommander commented 5 years ago

I have the same issue on Windows 10.

chrishuges commented 5 years ago

I assume this is because the data is a mix of targeted and dda. I imagine the targeted data is causing the issue. Is it possible to share the raw file (or any raw file with the same scan type) to help solve the issue?