Processing Error
Opened this issue · 8 comments
Hi,
I encountered a problem while running pGlyco3.
How should I solve it?
Many thanks.
This is fine, this is just a warning exception in pGlycoSite. The results were generated in the output folder
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!
Maybe your pGlyco version is expired, you need to download the new version at https://github.com/pFindStudio/pGlyco3/releases
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!
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.
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.
Yes, I checked .NET version, and it seemed not the reason of error. Could I got another advice? Thank you!
Try pGlyco_setup.exe in the release page?