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/CAGJJY%3D8DMJd01BXfS45apGun2%3Dx30Gz7uQa4%2B0Jr0E%3D-aFE7bA%40mail.gmail.com.
