[PYI-28260:ERROR] Failed to execute script 'MultiProcess' due to unhandled exception!

[DennisDannecker]

Hey guys,

I am trying to run pLink3 three on my Astral FAIMS data set with a BS3 crosslinker.

I run into this issue:

[MultiProcess] "Z:\user\Dennis\plink3\pLink_3_test_run\pLink_3_test_run.plink"
[MultiProcess] Start...
[MultiProcess] searcher.exe: C:\pFindStudio\pLink\3.0.17\bin\searcher.exe
[MultiProcess] Start 0 Z:\user\Dennis\plink3\pLink_3_test_run\tmps\multi\0\pLink.plink
[pLink] Welcome to use pLink v3.0.17, it will be expired on 20280110
[pLink] Search Engine initializing...
[pLink] Generating reverse database...
[pLink] Search identifier: KWYWR
[pLink] Search Engine is ready to search.

[pLink] Start searching Z:\ms\Astral_2\Dennis\20250915\20250915_A2_N1_Pachano_Stark_Dannecker_IMP_THIDxlms_01_2mM_cl_HCDAST.pf2, Labeling None
[pLink] Total spectra: 1071701724
[pLink] Loaded 5000 spectra, 5000 / 1071701724
[pLink] Loaded 5000 spectra, 10000 / 1071701724
[pLink] Loaded 5000 spectra, 15000 / 1071701724
[pLink] Loaded 5000 spectra, 20000 / 1071701724
[pLink] Loaded 5000 spectra, 25000 / 1071701724
[pLink] Loaded 5000 spectra, 30000 / 1071701724
[pLink] Loaded 5000 spectra, 35000 / 1071701724
[pLink] Loaded 5000 spectra, 40000 / 1071701724
[pLink] Loaded 5000 spectra, 45000 / 1071701724
[pLink] Loaded 5000 spectra, 50000 / 1071701724
[MultiProcess] Completed 0 Z:\user\Dennis\plink3\pLink_3_test_run\tmps\multi\0\pLink.plink
[ERROR] terminate called after throwing an instance of 'std::runtime_error'
what():
at IonIndexFlow::preprocessSpectra() spectra preprocess failed!
at IonIndexFlow::run() run ion-index flow failed!
at Searcher::searchTask() caught an exception.
terminate called recursively
[MultiProcess] 0, rank1 pfd number error
Traceback (most recent call last):
File "MultiProcess.py", line 78, in
File "MultiProcess.py", line 70, in _main
File "mp_flow.py", line 654, in mp_flow.flow_auto
File "mp_flow.py", line 535, in mp_flow.copy_rank1_rename
AssertionError: rank1 pfd number error
[PYI-28260:ERROR] Failed to execute script 'MultiProcess' due to unhandled exception!

Two things I will say:

There are definitely no chinese characters in any of the paths.
Also, the number of spectra pLink has identified and is trying to load in appears why to high:

[pLink] Total spectra: 1071701724

No way I have recorded over a billion spectra...what?
Is the counting off? I've checked on FreeStyle, and the number of spectra (MS1 and MS2) is closer to 191967, this also tracks better with the file size of about 6 GB.

Maybe you can help me figuring out what is going out and how to get it to run.

Thank you for your support.

Best
Dennis

[NorthblueM]

Dear Dennis,

I also think it's impossible to have 1071701724 extracted spectra.

Although pLink 3 supports the identification of chimeric spectra, meaning one MS2 spectrum can have multiple precursors, the extract is usually only increased by a few-fold. For example, with 191,967, the searched spectra are at most several hundred thousand, or just over 1 million.

One potential issue I can think of is that in some language settings, such as French or German systems, a comma (,) is used as the decimal separator instead of a dot (.). Please check the system's language/locale settings.

In addition, you could try searching a small raw file from an Astral or Orbitrap instrument, such as Lumos or Exploris 480, to see if pLink3 works successfully and rule out any operating system-related influences.

Regarding the search of cross-linked, ultra-large Astral raw data, please also refer to another issue: #27 . We expect to release a newly architected version of pLink3 within this year, which will fully support Astral data. If needed, you are welcome to contact us for early access.

Regards,
Pengzhi

[DennisDannecker]

Hi Pengzhi,

Thank you very much for your quick reply, much appreciated.

That's a good point regarding the decimal separator...might be mixed with dot at comma.

I will check with a smaller Astral dataset and see whether I can get it to run and will report back here.

Absolutely, I would very much appreciate early access to the announced newly deviced version of pLink3 that is more dedicated to Astral data. So yes, please do reach out, I am more than happy to test it.

Cheers,
Dennis