Processing Error

[onionbunny]

Hi,

I encountered a problem while running pGlyco3. How should I solve it?

Many thanks.

[jalew188]

This is fine, this is just a warning exception in pGlycoSite. The results were generated in the output folder

[onionbunny]

Thank you！While recently encountered a new problem, why does pGlycoSite give an error? How could I make it？

Process ID=16184: [pGlyco] Loading protein sequences ... Process ID=19988: [pGlyco Error] bad allocation Process ID=19988: D:\pGlyco3.0_build20231220\bin>gpPercolator.exe -p "D:\results_pglyco\20240107\AN_HC_p_G\process1\pGlyco.cfg" Process ID=19988: D:\pGlyco3.0_build20231220\bin>pGlycoFDR.exe -p "D:\results_pglyco\20240107\AN_HC_p_G\process1\pGlyco.cfg" Process ID=19988: Could not open D:\results_pglyco\20240107\AN_HC_p_G\process1\pGlycoDB-GP-Raw1.txt! Process ID=19988: D:\pGlyco3.0_build20231220\bin>pGlycoProInfer.exe -p "D:\results_pglyco\20240107\AN_HC_p_G\process1\pGlyco.cfg" Process ID=19988: Traceback (most recent call last): Process ID=19988: File "pGlycoProInfer.py", line 165, in Process ID=19988: File "pGlycoProInfer.py", line 140, in Run Process ID=19988: File "pGlycoProInfer.py", line 47, in ReadPeptide Process ID=19988: FileNotFoundError: [Errno 2] No such file or directory: 'D:\results_pglyco\20240107\AN_HC_p_G\process1\pGlycoDB-GP-FDR.txt' Process ID=19988: [4048] Failed to execute script 'pGlycoProInfer' due to unhandled exception!

[jalew188]

Maybe your pGlyco version is expired, you need to download the new version at https://github.com/pFindStudio/pGlyco3/releases

[onionbunny]

Thank you, but I used the latest version, and this occurs when choose 'HCD+EThcD', as log below:

Process ID=38024: [pGlyco Error] Open in CMGFReader: Could not open file: E: …… Process ID=37212: ??????????????: System.IO.FileNotFoundException: ??????????????????????Base, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null???????????????????????????????????????????? Process ID=37212: ?? CombineMS2.Program.Main(String[] args) Process ID=41544: [pParse] - Closed E:

I have tested several times, could I get some advice? Thanks!

[jalew188]

Ahh, it is bad allocaiton error from pGlycoDB kernel. Maybe you need to remove all other files except for RAW files. And then process the the raw data again.

[jalew188]

Thank you, but I used the latest version, and this occurs when choose 'HCD+EThcD', as log below:

Process ID=38024: [pGlyco Error] Open in CMGFReader: Could not open file: E: …… Process ID=37212: ??????????????: System.IO.FileNotFoundException: ??????????????????????Base, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null???????????????????????????????????????????? Process ID=37212: ?? CombineMS2.Program.Main(String[] args) Process ID=41544: [pParse] - Closed E:

I have tested several times, could I get some advice? Thanks!

Maybe it is the issue of .NET version, mine is .NET framework 7.0.x. You can check by dotnet --version.

[onionbunny]

Yes, I checked .NET version, and it seemed not the reason of error. Could I got another advice? Thank you!

[jalew188]

Try pGlyco_setup.exe in the release page?