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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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FragPipe-PDV viewer "Invalid spectrum file path, please check it" #1655

Closed rugenni closed 2 months ago

rugenni commented 2 months ago

log_2024-07-01_16-12-19.zip

Hi,

I processed three timsTOF .d files with FragPipe 22 using the LFQ-phospho workflow. When I try to open Fragpipe-PDV I get the error message "Invalid spectrum file path, please check it". All files are located within the same folder, I did not move any file. I noticed some warnings during PTMProphet like "chmod 664 interact-Steffi_A_rank5.mod.pep.xml" failed: Operation not permitted". Is this a known problem? (I ran FragPipe on a Windows 10 PC as Administrator).

Many thanks, Nils

fcyu commented 2 months ago

@KaiLiCn , could you take a look when you get a chance?

Note that it is a DDA+ search with the ddaPASEF data. PDV was supposed to look at the *_uncalibrated.mzML files, and there were multiple ranks per scan.

Best,

Fengchao

KaiLiCn commented 2 months ago

Hi Nils,

Could you also share the Fragpipe.workflow file inside your result folder with me?

Kai

rugenni commented 2 months ago

Hi Kai,

here it comes: fragpipe_workflow.zip

Thanks, Nils

KaiLiCn commented 2 months ago

Hi Nils,

I fixed the bug. Could you try the latest version of FragPipe-PDV? You could find it here: https://github.com/Nesvilab/FragPipe-PDV/tree/V1.2.2 . There is a README showing how to update it mannually inside FragPipe. We also update a tutorial file. You could find everything there.

Let me know if you have any iusse when you update it.

Kai

rugenni commented 2 months ago

Hi Kai and Fengchao,

thank you very much for your quick help, everything is working now.

Best, Nils

fcyu commented 2 months ago

Fixed in https://github.com/Nesvilab/FragPipe/commit/9c205796f647e03daab587258313c46afc0503ea