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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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"Not a valid pathDir for Bruker data directory" #1707

Closed Arthfael closed 3 months ago

Arthfael commented 3 months ago

Hi,

My search on simple QC files is failing with the following error:

...
Failed in checking D:\MyPath\HeLa_std_GA1_1_5474.d. Will ignore it.
Failed in checking D:\MyPath\HeLa_std_GA1_1_5477.d. Will ignore it.
Not a valid pathDir for Bruker data directory
Failed in checking D:\MyPath\HeLa_std_GA1_1_5472.d. Will ignore it.
Failed in checking D:\MyPath\HeLa_std_GA1_1_5475.d. Will ignore it.
Not a valid pathDir for Bruker data directory
Failed in checking D:\MyPath\HeLa_std_GA1_1_5476.d. Will ignore it.
Not a valid pathDir for Bruker data directory
Not a valid pathDir for Bruker data directory
Failed in checking D:\MyPath\HeLa_std_GA1_1_5473.d. Will ignore it.
Not a valid pathDir for Bruker data directory
Not a valid pathDir for Bruker data directory
Failed in checking D:\MyPath\HeLa_std_GA1_1_5471.d. Will ignore it.
Not a valid pathDir for Bruker data directory
There are corrupted files. Please remove those files and re-start the task.
Checking spectral files...
D:\MyPath\HeLa_std_GA1_1_5474.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5471.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5476.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5472.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5473.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5475.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
D:\MyPath\HeLa_std_GA1_1_5477.d: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = []
Process 'MSFragger' finished, exit code: 1
Process returned non-zero exit code, stopping

This would suggest that there is an issue with the .d folders, yet they look normal to me: Bruker_file

I have tried to convert the files to mzML to see if maybe that would work. Here is the outcome:

C:\> "C:/PROGRA~1/ProteoWizard/ProteoWizard 3.0.22339.3ffd5e2/msconvert.exe" -f tmp_MS_files.txt -o "D:/MyPath" --mzML --64 -z --filter "peakPicking true 1-"
format: mzML 
    m/z: Compression-Zlib, 64-bit
    intensity: Compression-Zlib, 64-bit
    rt: Compression-Zlib, 64-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: D:/MyPath
extension: .mzML
contactFilename: 
runIndexSet: 

spectrum list filters:
  peakPicking true 1-

chromatogram list filters:

filenames:
  D:/MyPath/HeLa_std_GA1_1_5471.d
  D:/MyPath/HeLa_std_GA1_1_5472.d
  D:/MyPath/HeLa_std_GA1_1_5473.d
  D:/MyPath/HeLa_std_GA1_1_5474.d
  D:/MyPath/HeLa_std_GA1_1_5475.d
  D:/MyPath/HeLa_std_GA1_1_5476.d
  D:/MyPath/HeLa_std_GA1_1_5477.d

processing file: D:/MyPath/HeLa_std_GA1_1_5471.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5471.d

processing file: D:/MyPath/HeLa_std_GA1_1_5472.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5472.d

processing file: D:/MyPath/HeLa_std_GA1_1_5473.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5473.d

processing file: D:/MyPath/HeLa_std_GA1_1_5474.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5474.d

processing file: D:/MyPath/HeLa_std_GA1_1_5475.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5475.d

processing file: D:/MyPath/HeLa_std_GA1_1_5476.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5476.d

processing file: D:/MyPath/HeLa_std_GA1_1_5477.d
SQLITE_CANTOPEN[14]: unable to open database file
Error processing file D:/MyPath/HeLa_std_GA1_1_5477.d

As far as I know, the only specificity of these files is that immediately before acquiring them we switched from using a nanoElute 2 to an Ultimate 3000 nano as the HPLC. Could this be causing issues with the method? Is there something which we would need to configure in the Bruker software for these to run correctly? The Bruker ProteoScape search also failed (which could mean anything, seeing how it randomly fails for a lot of stuff - but in this case does work as further supporting evidence that something isn't quite right).

fcyu commented 3 months ago

Since all three software not just MSFragger failed in processing your data, you probably need to double check your data acquisition parameters.

Just in case , you need to have the Visual C++ Redistributable installed to make the Bruker's library work. It probably isn't the cause of the errors because most Windows operating systems already have it installed.

Best,

Fengchao

Arthfael commented 3 months ago

Yes, sorry, I guess I figured out that the problem may be at an earlier level as I was writing the error report and trying a few things to provide more info. Still, I hoped that the FP error may shed some light on the cause of the issue.

On Mon, Aug 5, 2024 at 4:33 PM Fengchao @.***> wrote:

Since all three software not just MSFragger failed in processing your data, you probably need to double check your data acquisition parameters.

Just in case , you need to have the Visual C++ Redistributable https://aka.ms/vs/16/release/VC_redist.x64.exe installed to make the Bruker's library work. It probably isn't the cause of the errors because most Windows operating systems already have it installed.

Best,

Fengchao

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