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/a8fb66fa-c7aa-4533-9738-87fa68410d57n%40googlegroups.com.
