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AutoQC problem eversa  2020-07-23 13:11:49
 

Hi, I tried to run a AutoQC and got the below error message:

--in="C:\ZWC-autoQC\test.sky" --remove-before=6/23/2020 --import-file="C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw" --import-on-or-after=6/23/2020 --save
--panorama-server="https://panoramaweb.org/" --panorama-folder="Washington University STL - Evers Lab/AutoQC" --panorama-username="eversa@wustl.edu"
[7/23/2020 2:26:58 PM] Opening file...
[7/23/2020 2:26:59 PM] File test.sky opened.
[7/23/2020 2:27:00 PM]
[7/23/2020 2:27:00 PM] Adding results...
[7/23/2020 2:27:00 PM] 1. C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw
[7/23/2020 2:27:00 PM]
[7/23/2020 2:27:01 PM] ERROR: Error: Failed importing the results file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw.
[7/23/2020 2:27:01 PM] Message: pwiz.Skyline.Model.Results.MissingDataException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used. ---> pwiz.Skyline.Model.Results.NoFullScanFilteringException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used.
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.SpectraChromDataProvider..ctor(MsDataFileImpl dataFile, ChromFileInfo fileInfo, SrmDocument document, IRetentionTimePredictor retentionTimePredictor, String cachePath, IProgressStatus status, Int32 startPercent, Int32 endPercent, IProgressMonitor loader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 98
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateSpectraChromProvider(MsDataFileImpl dataFile, ChromFileInfo fileInfo) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1265
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 237
[7/23/2020 2:27:01 PM] --- End of inner exception stack trace ---
[7/23/2020 2:27:01 PM]
[7/23/2020 2:27:01 PM] ERROR: SkylineRunner.exe exited with code 0. Skyline document import failed.
[7/23/2020 2:27:01 PM] Adding C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw to the re-import queue.
[7/23/2020 2:27:01 PM] Attempting to re-import C:\ZWC-autoQC\ZWC_459_a1b3_30uMOPD_200719145246.raw.
[7/23/2020 2:27:01 PM] ZWC_459_a1b3_30uMOPD_200719145246.raw is ready
[7/23/2020 2:27:01 PM] Running SkylineRunner.exe with args:
[7/23/2020 2:27:01 PM]
 
 
Vagisha Sharma responded:  2020-07-23 15:05:11

Hi,

The error message is:

The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms.
To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used.

On what type of instrument was this data acquired? If this is full scan acquisition data then you will have to choose the appropriate settings under Settings > Transition Settings > Full-Scan in Skyline as the error message says. You could first try importing the raw data file into your document directly in Skyline without going through AutoQC Loader. Once you have figured out all the settings and have a template Skyline document you can automate raw data import with AutoQC Loader.

Thanks,
Vagisha