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 On Tue, May 28, 2024 at 7:27 PM Zeyu Wang <wangzeyuu...@gmail.com> wrote: > 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? > > [image: Snipaste_2024-05-28_22-14-14.png] > [image: Snipaste_2024-05-28_22-15-57.png] > > Best, > Zeyu > > > > > > On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote: > >> Hi David, >> >> Thanks! After replacing the current kojak.exe, It seems that now the >> kojak searching can continue without error message. >> >> Best, >> Zeyu >> >> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote: >> >>> 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 >>> >>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang <wangze...@gmail.com> wrote: >>> >>>> Hi David, >>>> >>>> Thank you! Here are the two kojak parameter files I tested (the >>>> original and the customized). Link: Kojak_Troubleshooting >>>> <https://gtvault-my.sharepoint.com/:f:/g/personal/zwang3136_gatech_edu/EnxqUYYUZGNDvCEG8kB-vtsB3Q2GfNvcqaAygJ_0ttBEFA?e=Ub1nub> >>>> . >>>> >>>> Best, >>>> Zeyu >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote: >>>> >>>> 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 >>>> >>>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang <wangze...@gmail.com> wrote: >>>> >>>> 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 >>>> >>>> -- >>>> 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 >>>> <https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>>> -- >>>> 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/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com >>>> <https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- > 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-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/db56c834-5f2b-486f-a160-9b3bf9228ed2n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/db56c834-5f2b-486f-a160-9b3bf9228ed2n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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