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