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Failed importing results (that previously could import) wphipps5  2023-11-23 07:09
 

Hello,

I am using Skyline-daily (64-bit) 23.1.1.318 (6096a599b) on Windows 10. I've tried to upload a zip (wphipps5_prm.zip with the Skyline documents and raw files) but I can't tell if it went through.

I am getting the following error message trying to import PRM data that previously successfully imported into Skyline:

Failed importing results file 'C:\Users\wphipps5\Desktop\New folder\STMS_20230613_heladigest02_PRM.raw'.

pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'C:\Users\wphipps5\Desktop\New folder\STMS_20230613_heladigest02_PRM.raw'.
---> pwiz.Skyline.Util.AssumptionException
at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\pwiz\pwiz_tools\Skyline\Util\Util.cs:line 2041
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.get_ChromIds() in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 556
at pwiz.Skyline.Model.Results.ChromCacheBuilder.<GetChromDataSets>d__38.MoveNext() in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 614
at System.Linq.Enumerable.<SelectManyIterator>d__172.MoveNext() at pwiz.Skyline.Model.Results.ChromCacheBuilder.CalcPeptideChromDataSets(ChromDataProvider provider, List1 listMzPrecursors, HashSet`1 setInternalStandards) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 525
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 375
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 256
--- End of inner exception stack trace ---

The file above in the error message is already in the document because 6 months ago it would successfully import. I am experiencing this error with newer samples and thus was retrying older files. Some older files work, others do not.

Thanks for any help
Bill Phipps, UW
 
 
wphipps5 responded:  2023-11-23 08:24

The error seems dependent on which version of Skyline I am using.

Skyline-daily (64-bit) 23.1.1.318 (6096a599b) <<< generates the error, whereas an earlier version of skyline does not

Skyline-daily (64-bit) 23.1.1.268 (c58f1f56e) <<< This version does not experience error message when importing the same files

I was able to confirm this further by downloading the non-daily version of Skyline-- Skyline-daily (64-bit) 23.1.1.318 (6096a599b), which also does not produce the error.
 
Nick Shulman responded:  2023-11-23 10:32
Oops. This seems to be a bug that I introduced into Skyline-daily a few weeks ago.
I can tell you that Skyline is getting confused by the pressure trace chromatograms that are available in the .raw file, and somehow Skyline is putting them in the wrong order in a big list.
I will try to figure out exactly what is going wrong and fix it.
For now, the only workaround for you really will be to use that previous build of Skyline-daily.

Thank you for reporting this bug.
-- Nick
 
wphipps5 responded:  2023-11-23 12:32
That would make sense. When I trace enough files back, any files generated after our move from Thermo EasyNano1000 LC to the Neo Vanquish generate the error. Whereas files before change in the chromatograph instrument don't produce the error.
Thanks