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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
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Cannot parse and output QE Orbitrap data #79

Closed EstrellaXD closed 2 years ago

EstrellaXD commented 2 years ago

Describe the bug

Only -x can output a txt file, but parse and other command cannot output any file.

Description of raw file Raw file was gen by QE Orbitrap, and can be read successfully by xcabliur. Metadata is here:

Instrument: Q Exactive Orbitrap
ExperimentMsOrder:  Ms
MS1Analyzer:    MassAnalyzerFTMS
MS2Analyzer:    Any
MS3Analyzer:    None
TotalAnalysisTime(min): 26.7562
TotalScans: 6004
NumMs1Scans:    6004
NumMs2Scans:    0
NumMs3Scans:    0
MeanMs2TriggerRate(/Ms1Scan):   0
Ms1ScanRate(/sec):  3.7399
Ms2ScanRate(/sec):  0
MeanDutyCycle(s):   0
MedianMs1FillTime(ms):  30
MedianMs2FillTime(ms):  0
MedianMs3FillTime(ms):  0
FaimsVoltage(CV):   -1
Ms2MedianSummedIntensity:   0
MedianMS1IsolationInterference: 0
MedianPeakWidthAt10%H(s):   0
MedianPeakWidthAt50%H(s):   0
MedianAsymmetryFactor:  0
PeakCapacity:   0
NumEsiInstabilityFlags: 0

File size: 150MB Command line arguments

mono /Users/Estrella/Developer/MS_Process/process/module/RawTools/RawTools.exe                                 -f /Users/Estrella/Developer/MS_Process/Data_Example/HeLa.RAW                                 -o /Users/Estrella/Developer/MS_Process/process/cache                                 -p -x

Command line output

This is not an Orbitrap file. Skipping reaction event extraction.

This raw file contains only MS1 scans.
...
File only contains MS1 scans. Skipping meta data calculations.

There are no dependent scans and therefore no matrix data to write to file.

Elapsed time: 1.99 s

Time to process all 1 files: 00:00:01.9956085

Desktop & RawTools information: