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wenbostar / PDV

PDV: an integrative proteomics data viewer
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Data loading issue #66

Closed YechenHu closed 8 months ago

YechenHu commented 8 months ago

Hi，

I have been attempting to utilize PDV to visualize Glyco-peptide database search results, but I encountered an issue during the data upload step. The files I uploaded were in mzML and pepXML formats. Additionally, the software has been stuck in the 'uploading data' state for over two weeks, and I am unable to close it.

Thank you for your assistance.

bug

KaiLiCn commented 8 months ago

Hi,

Sorry for the inconvenience. Please open theTask Manager, selectPDV thread and then End it. image

Now PDV only supports Glyco-peptide search results from FragPipe. Since the format changes in different version of FragPipe, I highly recommend you open the FP-PDV built inside the FragPipe after your search Open FragPipe-PDV Viewer. image

Please let me know if you have difficulties opening your result inside FragPipe.

YechenHu commented 8 months ago

Thank you for your prompt response! It seems that FP-PDV defaults to opening the most recent search results. How can I open earlier search results from other dates?

KaiLiCn commented 8 months ago

You just need to copy your result folder path in Output dir or Browse it to set it.

YechenHu commented 8 months ago

Thanks. However, regardless of whether I use the browse or paste the path, I still encounter an error: Invalid spectrum file path, please check it. I'm sure the path is correct, and I didn't move any result files out of that folder. I do add some files into that folder, is this the reason why?

KaiLiCn commented 8 months ago

Sorry, I can't see your screenshot.

YechenHu commented 8 months ago

Sorry about that. The error is: Invalid spectrum file path, please check it.

KaiLiCn commented 8 months ago
  1. Can you share your latest .log file with me?
  2. Can you check the mzML file path in *.manifest file inside your result folder?
YechenHu commented 8 months ago

Please find my latest .log file and screenshot of my result folder. log_2023-12-15_10-58-48.txt Screenshot 2024-01-04 result folder

KaiLiCn commented 8 months ago

Is it ok to share your whole folder with me? You could upload it here: https://www.dropbox.com/request/UISpGex3ISkS4muNPRLy

I can take a quick test once I recieve it.

YechenHu commented 8 months ago

Thanks, I've uploaded it.

KaiLiCn commented 8 months ago

Based on the files you shared with me, I found the mzML file path is different with what you shown in your screenshot. Here is the path in fragpipe-files.fp-manifest file. image Here is your screenshot. image

You probably moved your search result folder after your searching. Nothing wrong with your result. I can open it. You just need to change the mzML file path in the fragpipe-files.fp-manifest file, either absolute or reletive path with your result folder.