Array dimension Error

Array dimension Error dkueltz  2021-05-01 11:09:27

I am getting an error with the latest Skyline daily release that I had not seen before. This pops up when I import a results file with a large RT range specified. The assay library contains less than 200,000 transitions - so it should not be a problem. I did not see this error with previous versions even though the assay libraries I had used before were much larger (>1 million transitions). The error message is below. FYI - i am only allowing for about 15 or so PTMs in the corresponding document. I am using a workstation with 64GB RAM, which in my mind makes it unlikely that memory limitation is the issue. The results file import also crashed a couple of times already with the latest release and it kept hanging up on me when trying to close -reopen - I had to completekly uninstall and reinstall Skyline daily to render it to respond properly again - something seems to have changed that renders the import of results files more error-prone.
Thanks for looking into the array dimension limit errror pasted below,

At 10:57 AM:
Failed importing results file 'E:\EAM0025_Oremo-Testes_V8-AmBic\DIA\EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d'.
Array dimensions exceeded supported range.
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\EAM0025_Oremo-Testes_V8-AmBic\DIA\EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d'.
Array dimensions exceeded supported range. ---> System.OverflowException: Array dimensions exceeded supported range.
at pwiz.Skyline.Model.Results.ChromGroups.ReleaseChromatogram(Int32 chromatogramIndex, Single retentionTime, ChromCollector collector, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCollector.cs:line 625
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Collectors.ReleaseChromatogram(Int32 chromatogramIndex, ChromGroups chromGroups, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1298
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 609
at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 77
at pwiz.Skyline.Model.Results.ChromDataSet.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 234
at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 143
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 439
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252
--- End of inner exception stack trace ---

Nick Shulman responded:  2021-05-01 11:23:23

Can you send us your Skyline document and also zip up your raw file "EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d" and send it to us?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
Please send us that file as well the zipped up folder "EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d".

You can upload those files here:

When Skyline is extracting chromatograms, Skyline writes data out to a bunch of temporary files before everything eventually gets put into the .skyd file. The error that you are seeing is happening because one of the temporary files ended up being more than 2GB in size, and our code cannot handle it.
Skyline is supposed to choose how many chromatograms can fit into each temporary file, based on the number of scans in your raw file, so it's not supposed to be possible for the error that you are seeing to happen.
It sounds like there is an error in Skyline's estimate of how many points some chromatograms are going to have. After we see your files I imagine it will be straightforward for us to fix this.

Thanks for reporting this issue,
-- Nick