I installed Skyline-Daily, but unfortunately this opened up another issue on my side.
I'm able to open the file using Skyline-Daily GUI, however when I now use SkylineDailyRunner (or also the older SkylineRunner) I always get the following error :
Error: Failed importing the results file 20181025_OR12_Ag2_3522075_SA_PE_M51-Y_1,8ul.raw.
[2019-01-14 15:57:57] Message: System.IO.FileNotFoundException: Could not find file 'D:\forD\test\data\Library_centroid.skyd'.
File name: 'D:\forD\test_1fileD\data\Library_centroid.skyd'
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
at pwiz.Skyline.Util.FileStreamManager.CreateStream(String path, FileMode mode, Boolean buffered) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 584
at pwiz.Skyline.Util.PooledFileStream.Connect() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 419
at pwiz.Skyline.Util.ConnectionPool.GetConnection(Identity id, Func`1 connect) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 227
at pwiz.Skyline.Util.ConnectionId`1.get_Connection() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 332
at pwiz.Skyline.Util.PooledFileStream.get_Stream() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 472
at pwiz.Skyline.Model.Results.ChromatogramCache.Load(String cachePath, IProgressStatus status, ILoadMonitor loader, Boolean assumeNegativeChargeInPreV11Caches) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 562
at pwiz.Skyline.Model.Results.ChromatogramCache.Build(SrmDocument document, String documentFilePath, ChromatogramCache cacheRecalc, String cachePath, MsDataFileUri msDataFileUri, IProgressStatus status, ILoadMonitor loader, Action`2 complete) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 609
I've tested with other raw files, libraries as well as with SkylineRunner and always get the same type of error. This is the line I'm running:
"C:\Program Files\Skyline\SkylineDailyRunner.exe" --timestamp --dir="D:\forD" --in="Library_centroid.sky" --out="test_1fileD\data\Library_centroid.sky" --full-scan-rt-filter-tolerance=5
Is there something I should have changed when installing Skyline-Daily?
Thanks for your help,
I do not know what could be causing that error.
Skyline is trying to read the file:
The .skyd file contains the chromatograms that have been extracted from the raw file. I am not sure why Skyline is not able to find the file.
The command line that you were running when this error happened was:
"C:\Program Files\Skyline\SkylineDailyRunner.exe" --timestamp --dir="D:\forDonna" --in="test_1fileDonna\data\Library_centroid.sky" --import-process-count=3 --import-all="test_1fileDonna" --reintegrate-model-name="data" --reintegrate-create-model --reintegrate-overwrite-peaks --save --report-add="D:\forDonna\lfqbench\SWATHbenchmark_report.skyr" --report-conflict-resolution=overwrite --report-name=SWATHbenchmark --report-file="test_1fileDonna\data\SWATHbenchmark.csv" --report-invariant
Skyline extracted chromatograms from:
I am not sure whether Skyline successfully finished extracting chromatograms from that .raw file. It might be that there was a bug and Skyline tried reading from the .skyd file before Skyline was actually finished creating that file.
One thing that you could try doing is removing that "--import-process-count=3" part of the command line. That option tells Skyline to launch extra instances of itself in order to do the work of extracting chromatograms. I could imagine that if there is a timing issue causing a bug, the problem might
be fixed if you do not specify that option.
If you want to go back to using Skyline version 4.2, you can use Skyline-Daily to save your document in the previous version format.
In Skyline, you can use the menu item:
File > Share
and on the dialog that comes up, there is an option to save in the format of previous versions of Skyline.
Maybe someone else has a better idea what is going wrong for you.