pGlycoDB.exe stops working when extracting raw data

[lindaz711]

As stated in the subject, the program stopped working when extracting raw data. The related screen shots, windows temp files, and the modified enzyme configuration file were uploaded to the following link. Could someone please help me identify and solve the problem? Thank you.
https://www.dropbox.com/sh/v6oo1gx4r7h2rar/AABDCkS0kOboqXmhZbaQ-jfga

[jalew188]

@lindaz711 Please FULLY remove MSFileReader and then reinstall it with BOTH x64 and x86 version.
NOTE: using modify panel of msfilereader can lead to unwilling result, please fully uninstall MSFileReader.

[lindaz711]

@jalew188 , Thank you for your response. I did uninstall and reinstall MSFileReader with both 64 and x86. But pGlyco still won't extract the raw spectra only now it doesn't show an error message and just shows "Task complete" 10 seconds after I start a run.

@lindaz711 Please FULLY remove MSFileReader and then reinstall it with BOTH x64 and x86 version.
NOTE: using modify panel of msfilereader can lead to unwilling result, please fully uninstall MSFileReader.

[jalew188]

@lindaz711 From your screen shot, I see pGlyco crashed while "Ion Indexing". Did you use your self-built glycan database?

[lindaz711]

@jalew188 No, I didn't use any customized glycan database. But can I (sidetracked)? It would make pGlyco much more applicable for my data if I could load my own glycan databases.

[jalew188]

@lindaz711 In the next version!!

[jalew188]

@lindaz711 Could you give me a raw file to test?

[lindaz711]

@jalew188 <https://github.com/jalew188> I would but my raw files are about 4~5 GB each. Is there a good way that you'd recommend for sharing those files?

…

On Tue, Apr 2, 2019 at 4:27 AM Jalew ***@***.***> wrote: @lindaz711 <https://github.com/lindaz711> Could you give me a raw file to test? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#28 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AmmcT-n61v1AcxgeMnWXOZp8AshbRFxfks5vcxSMgaJpZM4cPHc2> .

-- Peng (Linda) Zhao Dr. Lance Wells' Laboratory Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens, GA 30602 Tel: (706) 542-9741 (Lab)

[jalew188]

@lindaz711 try a small mgf or http://pfind.ict.ac.cn/download/pGlyco/07-all-energy-All_in_One_HCDFT.mgf to check if pGlyco works.

[lindaz711]

@jalew188 I extracted my raw files into mzML using ProteoWizard and pGlyco seems to be able to process the mzML files. I guess it just couldn't process raw files anymore.

[jalew188]

@lindaz711 Try to remove any intermediate file (for example, .csv, .xtract files) in the raw folder and run pGlyco again.

[lindaz711]

@jalew188 I don't keep any intermediate files in the same folder as the raw files especially when I start a new run. But it still doesn't seem to be working with extracting raw files.

[jalew188]

@lindaz711 You may need to e-mail to pparse.@ict.ac.cn to ask for a new pParse.

[lindaz711]

@jalew188 Actually I got it to work once I renamed the "xtract_msfilereader" to "xtract_raw". Didn't realized that pGlyco only calls for "xtract_msfilereader" since both .exe files are in the bin folder. The bottom line is that it works now! Thanks for everything.