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.
Describe the bug
I tried to run two raw files trough the tool with a X!Tandem search enabled. Without it everything runs trough smoothely.
Description of raw file
relatively small and simply run. BSA 60 min gradient DDA.
Command line arguments
I used the GUI
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).
2 file(s) to process
Processing: C:\Users\50112675\Documents\Test_rawtools\190506_BSA_10.raw
Determing MS analysis order... Done!
Extracting scan indices: 100%
Checking for orphaned scans: 100%
================ Scan indexing report ================
Total scans in file: 9089
Scans linked: 9089
Orphan scans:
None!
All scans accounted for!
======================================================
Extracting reaction events: 100%
Extracting scan data: 100%
Extracting trailer extras: 100%
Extracting precursor masses: 100%
Extracting retention times: 100%
Analyzing precursor peaks: 100%
Refining precursor charge and monoisotopic mass: 100%
Calculating meta data
MS1 isolation interference
MS2 scan cycle density
Ion injection time
Duty cycle
Intensity distribution
Summed intensities
Calculating metrics
Writing MGF file: 100%
Writing Ms TIC chromatogram: 0%
Writing Ms TIC chromatogram: 100%
Writing Ms base peak chromatogram: 0%
Writing Ms base peak chromatogram: 100%
Writing Ms TIC chromatogram: 0%
Writing Ms TIC chromatogram: 100%
Writing Ms base peak chromatogram: 0%
Writing Ms base peak chromatogram: 100%
Writing MGF file: 100%
Reading FASTA file
Writing target-decoy database: 100%
X! TANDEM Alanine (2017.2.1.4)
Loading spectra| (mgf).. loaded.
Spectra matching criteria = 3868
Starting threads .|.|. started.
Computing models:
t
waiting for 2|3| done.
sequences modelled = 0 ks
Model refinement:
waiting for 2|3| done.
Merging results:
from 2.3.
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
Valid models = 399
Unbehandelte Ausnahme: System.IndexOutOfRangeException: Index was outside the bounds of the array.
at RawTools.Utilities.AdditionalMath.Percentile(Double[] Values, Int32 percentile) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Utilities\Utilities.cs:line 322
at RawTools.QC.SearchQC.ParsePSMs(SearchMetricsContainer searchMetrics, PsmDataCollection psmCollection, WorkflowParameters parameters) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\QC\SearchQC.cs:line 239
at RawTools.QC.SearchQC.ParseSearchResults(SearchMetricsContainer searchMetrics, WorkflowParameters parameters, String rawFileName) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\QC\SearchQC.cs:line 73
at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\WorkFlows\DDA.cs:line 155
at RawTools.Program.DoStuff(UniversalOptions opts) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Program.cs:line 656
at CommandLine.ParserResultExtensions.WithParsed[T](ParserResult`1 result, Action`1 action)
at RawTools.Program.Main(String[] args) in C:\Users\Kevin\Documents\GSC\Projects\RawTools\RawTools\Program.cs:line 69
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop & RawTools information:
OS: Win 10
RawTools version: 1.0.0
Additional context
Add any other context about the problem here.
Describe the bug I tried to run two raw files trough the tool with a X!Tandem search enabled. Without it everything runs trough smoothely.
Description of raw file relatively small and simply run. BSA 60 min gradient DDA.
Command line arguments I used the GUI
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).
Screenshots If applicable, add screenshots to help explain your problem.
Desktop & RawTools information:
Additional context Add any other context about the problem here.