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.
On Monday, April 6, 2020 at 12:39:33 PM UTC-7, Lindsey Ulmer wrote: > > 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 <[email protected]> >> 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 >>> >>> -- >>> 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/7b61c92d-eada-4313-bef9-267e4f5d06a0%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/spctools-discuss/7b61c92d-eada-4313-bef9-267e4f5d06a0%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/7e21de6c-de7f-46c9-bab0-aa409a187479%40googlegroups.com.
