Filtered mzML crashes due to scan numbers?

[glormph]

Hi, I have a filtered mzML file (Thermo) for testing, wich contains scan numbers 10000-10500. When I run luciphor, it crashes quickly and complains as follows:

  spectra.mzML:  Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at com.simontuffs.onejar.Boot.run(Boot.java:340)
        at com.simontuffs.onejar.Boot.main(Boot.java:166)
  Caused by: umich.ms.fileio.exceptions.FileParsingException: No such scan number found in the index [10001]
        at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parseScan(AbstractXMLBasedDataSource.java:671)
        at lucxor.globals.read_mzML(globals.java:685)
        at lucxor.globals.read_in_spectra(globals.java:655)
        at lucxor.LucXor.main(LucXor.java:70)
        ... 6 more

I suspect it has something to do with the scans being filtered (msconvert --filter "scanNumber 10000-10500" ... ), but I don't really know if this is the problem. If anyone has a hunch, I'd like to hear it. :)

[dfermin]

That would be my first guess looking at that error.
What happens if you don't filter the mzML file? Does it run as expected?

[glormph]

I tested with filtering the first 500 scans (which are crap), and then it doesnt crash on reading the spectra. (I can run the full file, but that'll take a while)

[dfermin]

It might be that it's barfing because the new mzML file starts at 10000 instead of 1. See if you can run it with the first 1000 or 5000 scans.

[glormph]

Yeah, it's just that I'm trying to keep small test data (first 1000 scans is also giving really bad PSMs), so I think I'll try to re-number the scans instead, if I manage to do so by regex or something.

Could this be issue with an underlying mzML reading library then?

[dfermin]

That's what I suspect based on the error message and what you're telling me here.

[glormph]

Ok, thanks for the quick replying! Will try to re-number.