• Sign In
  1. Requests

Error Exporting to MassLynx Only with Scheduled Method

support

View Request

view list print
Error Exporting to MassLynx Only with Scheduled Method cbm11  2024-02-22 01:28
 
Good morning,
I have quite a large document with ~1000 peptides which I want to develop a method for, so I split them into a few 10 min runs with RepLiCal RT Predictor and am now using that to predict RT and schedule them all in one much longer run. The issue is that I am getting this error (which I assume might be a MassLynx problem?) but it only occurs when I try to export the method as "Scheduled", I am able to export the method with no issues if I just export it as standard unscheduled. I am also able to export other scheduled documents as expected, this one in particular using RT prediction just throws up the error. I was wondering if you could help me out with this problem please? Thank you!

(I am sharing the Skyline doc on fileshare as "RT Prediction Export Issues" too)

---------------------------

An error occurred attempting to export.
Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\Gez.PRO\ACQUDB\BCR 2 SRM Plus IStd.exp" "D:\ColleenM.PRO\ACQUDB\rgi0ks4h.fwn\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB
---------------------------
OK More Info
---------------------------
System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\Gez.PRO\ACQUDB\BCR 2 SRM Plus IStd.exp" "D:\ColleenM.PRO\ACQUDB\rgi0ks4h.fwn\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB ---> System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\Gez.PRO\ACQUDB\BCR 2 SRM Plus IStd.exp" "D:\ColleenM.PRO\ACQUDB\rgi0ks4h.fwn\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_23_1\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 181
   at pwiz.Skyline.Util.Extensions.UtilProcess.RunProcess(ProcessStartInfo psi, String stdin, String messagePrefix, IProgressMonitor progress, IProgressStatus& status) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Util\Extensions\UtilProcess.cs:line 45
   at pwiz.Skyline.Model.MethodExporter.ExportMethod(String exeName, List`1 argv, String fileName, String templateName, Dictionary`2 dictTranLists, IProgressMonitor progressMonitor) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Export.cs:line 4731
   at pwiz.Skyline.Model.WatersMethodExporter.ExportMethod(String fileName, String templateName, IProgressMonitor progressMonitor) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Export.cs:line 4523
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_23_1\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_23_1\pwiz_tools\Skyline\Util\Util.cs:line 1922
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 204
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.FileUI.ExportDlgProperties.PerformLongExport(Action`1 performExport) in C:\proj\skyline_23_1\pwiz_tools\Skyline\FileUI\ExportMethodDlg.cs:line 2313
---------------------------
 
 
Nick Shulman responded:  2024-02-22 06:59
You should make sure that you are running the latest version of Skyline 23.1.0.380.

The Skyline 23.1 that we released last autumn had a problem which would cause this error whenever you tried to export a Waters method.
The Skyline 23.1 that we released last month fixed that problem.

-- Nick
 
cbm11 responded:  2024-02-22 09:06
Hi Nick,
This is using the most recent version of Skyline (23.1.0.380), we did experience the problem with the earlier version, but we downloaded the newest version and it has been working fine. Except now, where oddly this is coming up with the newer version only for this one document, and only when I try to export it as a scheduled method (standard works)
 
cbm11 responded:  2024-02-22 10:18
Small update on this - when I check "use measured retention times" it will allow me to export a scheduled MassLynx method from this document.
It will also let me export the predicted RTs as a transition list (which unfortunately I don't think I can import into MassLynx MRM?).
So it appears I only get this error when I'm trying to export the method as a MassLynx .exp when using predicted RTs.
 
Nick Shulman responded:  2024-02-22 11:49
Can you send us your method template file (.exp) and your Skyline document?
I see that you uploaded a .zip file containing some Waters raw file folders and some files for a Skyline document but the Skyline document is missing a few files including its spectral library.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms, spectral libraries and iRT database.

Files which are less than 50MB can be attached to this support request. You can upload larger files to the same place that you did before:
https://skyline.ms/files.url

You wouldn't happen to also be getting an error when you do "File > Export > Isolation List", would you? It is really easy for us to debug problems with "Export > Isolation List". In order to debug a "Export > Method" problem we usually have to find a computer that has all the right Waters software on it, and that can take several days.
-- Nick
 
cbm11 responded:  2024-02-22 13:48
Hi Nick,
I've uploaded the correct .zip file and also .exp template file. Unfortunately there's no errors when I export an isolation list

Colleen
 
Nick Shulman responded:  2024-02-22 17:02

Can you try exporting the method using Skyline-daily instead of Skyline 23.1?
Back in October we made a change to Skyline-daily so that it will include a lot more information in the error message when Method Export fails.
When you hit an error like this in Skyline-daily and press the "More Info" button, the text in there should have more of the output indicating why "BuildWatersMethod" failed.

Skyline message boxes usually have a copy button in the lower left corner which will copy the entire text of the message including what gets shown when you push the "More Info" button.
-- Nick
 
cbm11 responded:  2024-02-26 05:16
Hi Nick,
I had a look at exporting the method on Skyline-daily, same error, here is the info:

---------------------------

---------------------------
An error occurred attempting to export.
Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\ColleenM.PRO\ACQUDB\CADPanel_lIGHTANDhEAVY_300722_0001.exp" "D:\ColleenM.PRO\ACQUDB\lic1ceos.ra4\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB
---------------------------
OK More Info
---------------------------


System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\ColleenM.PRO\ACQUDB\CADPanel_lIGHTANDhEAVY_300722_0001.exp" "D:\ColleenM.PRO\ACQUDB\lic1ceos.ra4\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB ---> System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\ColleenM.PRO\ACQUDB\CADPanel_lIGHTANDhEAVY_300722_0001.exp" "D:\ColleenM.PRO\ACQUDB\lic1ceos.ra4\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB ---> System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\ColleenM.PRO\ACQUDB\CADPanel_lIGHTANDhEAVY_300722_0001.exp" "D:\ColleenM.PRO\ACQUDB\lic1ceos.ra4\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB

Output:
MESSAGE: Exporting method SkylineDailyTest]_0001.exp
Generating Waters MRM method file
Generating Quanpedia databank with input data.
...
Error generating Quanpedia databank
   at VerifyESkylineLibrary.OperationManager.GenerateDataBank(DataTable dataTable, Int32 rtWindow, String _dbName, Int32 nIonMode)ERROR: Error generating Quanpedia databank

 ---> System.IO.IOException: Error generating Quanpedia databank

Command-line: Method\Waters\BuildWatersMethod -w 1.5 -m "D:\ColleenM.PRO\ACQUDB\CADPanel_lIGHTANDhEAVY_300722_0001.exp" "D:\ColleenM.PRO\ACQUDB\lic1ceos.ra4\transitions.txt"
Working directory: D:\ColleenM.PRO\ACQUDB
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 188
   --- End of inner exception stack trace ---
   --- End of inner exception stack trace ---
   at pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 248
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 230
   at pwiz.Skyline.Util.Extensions.UtilProcess.RunProcess(ProcessStartInfo psi, String stdin, String messagePrefix, IProgressMonitor progress, IProgressStatus& status) in C:\proj\pwiz\pwiz_tools\Skyline\Util\Extensions\UtilProcess.cs:line 45
   at pwiz.Skyline.Model.MethodExporter.ExportMethod(String exeName, List`1 argv, String fileName, String templateName, Dictionary`2 dictTranLists, IProgressMonitor progressMonitor) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Export.cs:line 4928
   at pwiz.Skyline.Model.WatersMethodExporter.ExportMethod(String fileName, String templateName, IProgressMonitor progressMonitor) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Export.cs:line 4721
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz\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\pwiz\pwiz_tools\Skyline\Util\Util.cs:line 1922
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 204
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.FileUI.ExportDlgProperties.PerformLongExport(Action`1 performExport) in C:\proj\pwiz\pwiz_tools\Skyline\FileUI\ExportMethodDlg.cs:line 2352
---------------------------