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pFindStudio / pLink2

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
http://pfind.ict.ac.cn/software/pLink/index.html
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pLink2 Stuck running at start searching loading spectra #90

Open Rebennion opened 3 years ago

Rebennion commented 3 years ago

Hi,

pLink2 keeps getting stuck at this point below. I have checked that the files are in the folder ( See image, e.g. 2aRB_HCDFT.pf2). I have uninstalled and reinstalled MSFileReader. I would appreciate some help to troubleshoot this issue please.

I am running Windows 10 Pro. pLink Version: 2.3.9

Here is what the Output stalls at:

[pLink] Start searching E:\Mass Spec\Raw files2\2aRB_HCDFT.pf2, Labeling None [pLink] Total spectra: 65370 [pLink] Loaded 5000 spectra, 5000 / [65370] [pLink] Loaded 5000 spectra, 10000 / 65370 [pLink] Loaded 5000 spectra, 15000 / 65370 [pLink] Loaded 5000 spectra, 20000 / 65370

Plink2 Query

Thanks in advance for the assistance. Rebecca

K-Boum commented 3 years ago

Hi everyone,

I have encountered the same problem. Plink loads all the spectra from one file like Rebecca reports, then repeats starting with the welcome message and then crashes. It has been runnin succesfully on my computer in the past though.

Best, Michael

Update: The folder the data files were in was set to "read only". Solved the problem for me.

Zacharad commented 2 years ago

I'm having the same problem, the file wasn't set to "read only" in my case. Any luck @Rebennion with solving this?

NorthblueM commented 1 year ago

Hello, everyone

First of all, you need to make sure that you have read and write permissions in the folder where you store raw files, fasta files, and task result files, as well as in the pLink installation ./bin/ directory. You can test this by creating a new text file in the folder, writing something, and seeing if you can save the text file successfully.

Additionally, please monitor the memory usage of pLink when it is running. The memory may be insufficient if the database is too large. You can try to reduce the number of threads, or use a more powerful computer. You should also check the available disk space if you have a lot of data.

If the problem persists, you can send us the plink parameters and log files from your search task folder. The parameters file has a .plink suffix, and the log file is located at ./tmps/log.out.

Best regards.