Kojak File not Found

[Lindsey Ulmer]

Hi,

I've run Kojak with the same settings on other data files with no problem, but for some reason with this particular data file I keep getting the error that the pep.xml file cannot be found and am not sure why this one file would be different.

Thanks!

Lindsey

[Luis Mendoza]

Hi Lindsey,

It seems that Kojak did not finish successfully, and it may be the reason why there is no output file.  If you scroll down in the command-line output sub-window (the one in your screenshot, just scroll down more), you should be able to see diagnostic messages that may be helpful in troubleshooting the issue.

Cheers,

--Luis

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[Lindsey Ulmer]

The screenshot shows all that's in the command-line output sub-window. It stops while mapping precursors and gives no further diagnostic messages. Any reasons it would stop running?

On Monday, March 30, 2020 at 1:33:18 PM UTC-7, Luis wrote:

Hi Lindsey,

It seems that Kojak did not finish successfully, and it may be the reason why there is no output file.  If you scroll down in the command-line output sub-window (the one in your screenshot, just scroll down more), you should be able to see diagnostic messages that may be helpful in troubleshooting the issue.

Cheers,

--Luis

On Fri, Mar 27, 2020 at 2:27 PM Lindsey Ulmer <ulmerli...@gmail.com> wrote:

Hi,

I've run Kojak with the same settings on other data files with no problem, but for some reason with this particular data file I keep getting the error that the pep.xml file cannot be found and am not sure why this one file would be different.

Thanks!

Lindsey

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To unsubscribe from this group and stop receiving emails from it, send an email to spctools...@googlegroups.com.

[Michael Hoopmann]

I think you found a bug. There is some rare property of a particular precursor scan in that file that Kojak isn't handling correctly. I'll probably need access to that particular mzML file to identify the bug. I'll reach out to you by email.

[Michael Hoopmann]

Thanks for sending me the file, I was able to replicate the bug. It has been fixed in the newest version of Kojak. For those with similar problems, the newest Kojak can be found here: http://www.kojak-ms.org/download.html

Instructions for manually upgrading your Kojak before the next TPP release (Windows instructions):

2.       Go to C:\TPP\bin and rename Kojak.exe to Kojak.backup.

3.       Open the zip file you downloaded from the Kojak website and extract Kojak.exe into C:\TPP\bin