Issue with Kojak searching of TPP v7.0.0

[Zeyu Wang]

Hi,

Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the instruction and try to run a quick test. But at the very beginning, it reports an error. 

"Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, Institute for Systems Biology Visit http://kojak-ms.org for full documentation. ****** Begin Kojak Analysis ****** Time at start: Fri May 24 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 preconfigured crosslinkers. Reading FASTA database: c:/TPP/data/dbase/UP000005640_9606_20230222.fasta
...

  Total Proteins: 20594
  Adding Kojak-generated decoys. New Total Proteins: 41188
  5658462 peptides to search (2785870 linkable).

Fri May 24 02:52:45 2024 ERROR:
ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for output. Please ensure path and write permissions are correct."

Is the error due to the output file path format? Or shall I adjust the read/write permission of the TPP?

Best,

Zeyu

[David Shteynberg]

Hello Zeyu,

Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak in the latest release.  To help us troubleshoot this problem, would you mind sharing the parameter file used in your test?

Thank you!

-David

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com.

[Zeyu Wang]

Hi David,

Thank you! Here are the two kojak parameter files I tested (the original and the customized).  Link: Kojak_Troubleshooting .

Best,

Zeyu 

[David Shteynberg]

Hello again,

After a bit of digging I found that this is likely caused by a bug in the current TPP compiled and distributed version of Kojak that will have to be corrected for the next release.  Meanwhile you should be able to download and use the official Kojak build available here:  https://kojak-ms.systemsbiology.net/download.html

This version will require additional .net dependecies!

Please replace the current kojak executable in c:/TPP/bin with the executable from the zip file and try running kojak again.

Best of luck and keep us posted to your progress.

-David

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com.

[Zeyu Wang]

Hi David,

Thanks! After replacing the current kojak.exe, It seems that now the kojak searching can continue without error message.

Best,

Zeyu 

[Zeyu Wang]

Hi all,

I notice another small issue (maybe this is my win11 problem?): when running Kojak within TPP, I set the threads to 24 or 28. However, in the task manager, I notice the main search was always running on exact CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice similar problem?   

Best,

Zeyu 

[David Shteynberg]

Hello Zeyu,

Sorry I don't know the answer to your question but if it helps I corrected the issue you identified in the previously distributed version compiled with gcc for the TPP distribution installer.

I placed the gcc compiled version of Kojak.exe here: https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

Perhaps this one exhibits a different behavior when running multi-threaded.  In my tests the two version ran nearly at the same speed on my computer.

Cheers,

-David

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/db56c834-5f2b-486f-a160-9b3bf9228ed2n%40googlegroups.com.

[Zeyu Wang]

Hi David,

Thank you! I will replace the previous Kojak.exe (official build) with this new gcc compiled version and have a try.  

Best,

Zeyu  

[Zeyu Wang]

Hi David, 

I tested it with the new version. Now it works well, but CPU usage problem still exists. I change threads from 24, 20 to 16 and 8, but the TPP searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe running. 

Thanks again! Anyway, it can still run, though may take a bit longer time. 

Best,

Zeyu 

[David Shteynberg]

Hi Zeyu,

Thanks for testing this!  I recompiled another executable that should use more of the CPU during the search.  Can you please test it to see if this suits your needs?  Naturally, if you set the number of threads too high it might degrade the overall performance of your machine during the Kojak search.  

https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

It would interesting to compare the performance of before and after this change.  I am testing this on i9-13900H.

Cheers,

-David

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/637fa2e7-7f6d-4811-9537-858bd6bb540bn%40googlegroups.com.

[Zeyu Wang]

Hi David,

Sorry for the late reply. Later, I just left the computer running on E-cores, which took longer. Now I further tested the new kojak.exe you sent me, but it still doesn't change the default CPU usage.  

I believe this "feature" is due to how Windows handles task prioritization. I finally resolved it by adjusting the priority and affinity of Kojak.exe in the Windows Task Manager. 

Thanks for your help and advice!

Best,

Zeyu Wang

[David Shteynberg]

Hello Zeyu,

Would you mind installing the latest update and report back if you still have an issue here?

Thanks,

-David

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f6f97166-aaf6-4f83-a185-e2f01d63f48an%40googlegroups.com.

[David Shteynberg]

Zeyu,

I think I was reading your message from May, about the issue which you helped us identify and resolve, sorry.  Meanwhile,  I tested both MSVC default version of Kojak and compared to the one built for TPP using gcc and they seem completely equivalent in runtime.  Let me know if you observe something different.

Thank you,

-David

[Zeyu Wang]

 Hi David,

Thank you!  I see my name in the release note.  I'm glad I could help optimize TPP usage. 

Regarding the CPU usage issue, I believe it is related to my Windows setup and not to Kojak or its settings. Moreover, this issue is tolerable and does not significantly affect the time required for searches. 

Best,

Zeyu Wang