Problems saving mprophet features

Problems saving mprophet features rmagni  2021-02-19
Hello Skyline Team,

I am having troubles saving the mprophet features in csv. When I attempt to do so I see this message:

Failed attempting to save mProphet features to C:\Users\rmagni\Desktop\GMU_projects\Tuberculosis_DIA\TB_DIA_dilution_curve\try.csv.
Access to the path is denied.
OK More Info
System.Reflection.TargetInvocationException: Access to the path is denied. ---> System.UnauthorizedAccessException: Access to the path is denied.
   at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   at System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost)
   at pwiz.Skyline.Util.FileStreamManager.<>c__DisplayClass24_0.<Commit>b__1() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 713
   at pwiz.Skyline.Util.Helpers.TryTwice(Action action, Int32 loopCount, Int32 milliseconds) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1892
   at pwiz.Skyline.Util.FileStreamManager.Commit(String pathTemp, String pathDestination) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 715
   at pwiz.Skyline.Util.FileSaver.Commit(IPooledStream streamDest) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Util\UtilIO.cs:line 1217
   at pwiz.Skyline.FileUI.MProphetFeaturesDlg.WriteFeatures(String filePath, MProphetResultsHandler resultsHandler, IList`1 calcs, CultureInfo cultureInfo, Boolean bestOnly, Boolean includeDecoys, IProgressMonitor progressMonitor) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\MProphetFeaturesDlg.cs:line 146
   at pwiz.Skyline.FileUI.MProphetFeaturesDlg.<>c__DisplayClass13_1.<OkDialog>b__1(IProgressMonitor b) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\MProphetFeaturesDlg.cs:line 111
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1944
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.FileUI.MProphetFeaturesDlg.OkDialog() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\MProphetFeaturesDlg.cs:line 118

My goal is to have a final list of peptides and a q-value associated with them so that I don't have to refine manually. Am I doing the right thing trying to export the mprophet features or should I look for some other report?

Thank you very much and keep up the awesome work!

Nick Shulman responded:  2021-02-19
It looks like Skyline is having trouble writing to the filename that you have asked it to.
You might want to try restarting your computer, and then exporting the features to a completely different filename and folder on your computer.

The error that you are getting is similar to what this user was seeing a few months ago:

There are some useful suggestions about troubleshooting this issue in that other support request. We never did learn what was going wrong with that other computer, but if you send us some screenshots we might be able to figure out what is going wrong for you.
-- Nick
rmagni responded:  2021-02-22
Thank you for the reply. I tried what you said but even after restarting the computer it looks like anywhere I try to save it it gives me the same error. Anything that I try to export does not work, but I have no problem saving my analysis or spectral libraries.

Any other suggestion on how I can troubleshoot this?

Also, I am looking for templates/tutorials to run skyline from the command line, where can I find them?

Thanks again!

Brendan MacLean responded:  2021-02-22
Webinars 14 and 15:

Both include scripts that run Skyline in command-line mode. That is about as close as you will get to a tutorial. Otherwise, you can get full command-line documentation at Help > Documentation > Command Line in Skyline, or by simply running any of the command-line interface EXE files (SkylineRunner, SkylineDailyRunner, or SkylineCmd), but also by using the --help argument.

Hope this helps get you started.

So, this save failure only happens with the mProphet features? Or are you saying you get a similar error when you try to use File > Save?
rmagni responded:  2021-02-22
Thanks for the links, Brendan!

As far as my analysis File > Save works just fine. I can save my .sky, .skyd, .blib files with no issues.

On the other end File > Export does not work. No matter what I am trying to export, it always gives me the error 'Access to the path is denied'.


Brendan MacLean responded:  2021-02-22
That is very strange. So, even a transition list or a report gives you this access denied error? I can't immediately think of anything these methods have in common that is not true of File > Save, but that File > Save works is pretty important. It sounded like you also had no problem creating spectral libraries. Have you tried .irtdb (iRT calculator), .protdb (Background Proteome), .optdb (Optimization Library), Settings > Share, File > Share, Manage Reports - Share. Just trying to think of other operations that save files to disk. Maybe we will eventually see something that the cases that work on your computer do differently from the cases that don't.