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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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pLink getting stuck on "generating reverse database" #88

Closed amaralbc closed 3 years ago

amaralbc commented 3 years ago

Hello,

I've been using pLink for a while to process some runs but I ran into this issue today. When I hit start it goes the expected way, calls for MSFileReader, converts everything to MGF, but when it's about to start processing the software freezes on "generating reverse database" and it stays there running for hours. I tried to reprocess the same runs with the same fasta file that I successfully used last week, and I get the same error, which is weird. I've tried to reinstall MSFileReader, move folders, install everything on a different computer, and it still freezes at the exact same spot.

Here's the output:

  *********************************************
 /       pParse2.0 (x64) from pFind Studio     \
/        Email  :  pfind@ict.ac.cn              \
\        Website:  http://pfind.ict.ac.cn       /
  *********************************************

[pParse] Calling pXtract to export MS1 and MS2 files... [pParse] MS1list completes. [pParse] Processing 20210401_Paulo_17821_BSAx25_500ng_1.MS1 [pParse] CSV file already exists, pParse Complete! [pParse] == == == Time elapsed: 0 seconds. == == == = 

  *********************************************
 /       pParse2.0 (x64) from pFind Studio     \
/        Email  :  pfind@ict.ac.cn              \
\        Website:  http://pfind.ict.ac.cn       /
  *********************************************

[pParse] Calling pXtract to export MS1 and MS2 files... [pParse] MS1list completes. [pParse] Processing 20210401_Paulo_17821_BSAx25_500ng_2.MS1 [pParse] CSV file already exists, pParse Complete! [pParse] == == == Time elapsed: 0 seconds. == == == =
[pLink] Welcome to use pLink v2.3.9, it will be expired on 20230110 [pLink] Search Engine initializing... [pLink] Generating reverse database...

I've also tried with different fasta files thinking maybe something is wrong with my sequence, but even using a fasta containing only BSA I get the same error.

Any help would be much appreciated!

amaralbc commented 3 years ago

Okay, I think I've figured it out. The fasta file was on my OneDrive folder, and apparently this is an issue (even if it's available offline). Moving the fasta to any other folder (same or different hard drives, it doesn't matter) solved it and pLink works as expected. Don't know why this is a thing, but this fixed it for me.