thanks for the fast reply. The gap filler options are: PeakML.GapFiller(nSlaves=cores, filename = "combined_highintensity.peakml", ionisation = "detect", Rawpath = source.path,
outputfile = "highintensity_gapfilled.peakml", ppm=10, rtwin = 0
)
The console runs through my mzxml files ((Extracting peak data from PeakMl file,Peak data created in 692.179 s) and aborts with the given error message. The error occurs at the very end of the list of mzxml files. I hope this is a little bit more helpful.
Thanks
Daniel