| Brendan MacLean responded: |
2019-05-28 07:46 |
We are going to need that data file or one like it that causes this error. Please zip the .raw folder and post it to:
https://skyline.ms/files.url
Thanks for posting to the Skyline support board.
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| Brendan MacLean responded: |
2019-05-28 07:46 |
Also, please check that you can open this file with Waters MassLynx tools. If not, then it may just be a corrupted file.
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| nr412 responded: |
2019-05-28 07:53 |
Dear Brendan,
I did manage to open the datafile in Masslynx. It is sorted now as the file was not exported correctly before and hence the error.
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| nr412 responded: |
2019-05-28 07:53 |
Thanks so much for your response
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| warham responded: |
2024-12-12 16:17 |
Hi Nick,
I have this problem intermittently now from a Waters TQ Absolute that was exporting files just fine. Most files are still being read fine by skyline, all files appear normal in masslynx. I've attached the skyline files. These waters files are in folders, do you have an upload link that supports folder/directory uploads for the data, the files are quite small, but there are a lot of them.
Best,
Lance
This is the error message:
At 7:16 PM:
Failed importing results file 'L:__EXL_030\20241212_MRM_retake_new_samples\20241210-10.raw'.
[pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'L:__EXL_030\20241212_MRM_retake_new_samples\20241210-10.raw'.
[pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error ---> System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error
at pwiz.CLI.msdata.ReaderList.read(String filename, MSData result, Int32 runIndex, ReaderConfig config)
at pwiz.ProteowizardWrapper.MsDataFileImpl..ctor(String path, Int32 sampleIndex, LockMassParameters lockmassParameters, Boolean simAsSpectra, Boolean srmAsSpectra, Boolean acceptZeroLengthSpectra, Boolean requireVendorCentroidedMS1, Boolean requireVendorCentroidedMS2, Boolean ignoreZeroIntensityPoints, Int32 preferOnlyMsLevel, Boolean combineIonMobilitySpectra, Boolean trimNativeId) in C:\proj\skyline_24_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 200
at pwiz.Skyline.Model.Results.MsDataFilePath.OpenMsDataFile(Boolean simAsSpectra, Boolean preferOnlyMs1, Boolean centroidMs1, Boolean centroidMs2, Boolean ignoreZeroIntensityPoints) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\MsDataFilePath.cs:line 295
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 191
--- End of inner exception stack trace ---
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| Nick Shulman responded: |
2024-12-12 16:24 |
You can always upload files here:
https://skyline.ms/files.url
If you are uploading a bunch of small files, it is best to package them in a .zip file first.
-- Nick |
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| warham responded: |
2024-12-12 16:30 |
Just uploaded the -09 folder which does load, and the -10 folder which does not. |
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| Nick Shulman responded: |
2024-12-12 18:32 |
It is failing trying to read the three chromatogram-like things called "Sample Temp", "Column Temp" and "Room Temp".
Are you able to successfully see those things when you look at "20241210-10.raw" in MassLynx?
Can you send us a screenshot of what they look like in MassLynx? I am thinking that maybe they do not have any points in them, but I am not sure whether this is just the way the data is, or whether this is corrupted data.
I will ask my coworkers what we should do about this. It might be that we should ignore the fact that we are unable to get the data for these things and just continue on with reading the rest of the chromatograms.
-- Nick |
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| warham responded: |
2024-12-12 19:04 |
Here's a screenshot of some of the MRM the TICs with signal in sample -10. The tics for -09 and -10 are what they should be. And here's a screenshot of all the temps from both files. They all appear empty in masslynx for both -09 and -10. |
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| warham responded: |
2024-12-17 07:13 |
any better idea of what in the data collection might be tripping up the skyline import? |
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| Brian Pratt responded: |
2024-12-17 09:49 |
I don't have any advice to offer on the data collection side, but I can have a look at making Skyline more tolerant of the phenomenon. Hopefully the issue is with our own code, and not the reader DLL that Waters provides. I'll let you know what I find.
Brian Pratt |
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| Brian Pratt responded: |
2024-12-17 13:43 |
Are you certain that the -09 sample temps are empty, or just very low data point count? When converting to mzML with msconvert it looks to me like there is a single data point in the -09 "Sample Temp".
If I tweak our use of the Waters-supplied reader to ignore errors thrown when trying to read an empty channel, it seems to work OK - we still get the channel name and a zero-length chromatogram. But I need to convince myself that we aren't ignoring an actual problem with the file - I need to be sure that the channel really is empty, and the Waters reader is just overreacting.
Can you verify with the tools you have on hand?
Thanks
Brian Pratt |
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skyline_import_error.sky
skyline_temps_ts.jpg