No able to do Grouping based on condition sstoychev23513  2022-09-15 07:02
Hi guys,

I'm getting the following error when trying to group samples by condition... any suggestions?

Skyline version: (64-bit)
Installation ID: bdb00579-df5f-442a-82cc-2f7e2f5b8602
Exception type: AssumptionException
Error message: chromInfoData.ChromFileInfo is null


pwiz.Skyline.Util.AssumptionException: chromInfoData.ChromFileInfo is null
   at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Util\Util.cs:line 2080
   at pwiz.Skyline.Util.Assume.IsNotNull(Object o, String parameterName) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Util\Util.cs:line 2019
   at pwiz.Skyline.Controls.Graphs.RTReplicateGraphPane.RTGraphData.IsMissingAlignment(ChromInfoData chromInfoData) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\RTReplicateGraphPane.cs:line 366
   at pwiz.Skyline.Controls.Graphs.RTReplicateGraphPane.RTGraphData.IsMissingValue(TransitionGroupChromInfoData chromInfoData) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\RTReplicateGraphPane.cs:line 450
   at pwiz.Skyline.Controls.Graphs.SummaryReplicateGraphPane.GraphData.<>c__DisplayClass49_0`1.<MakePointPairLists>b__3(TChromInfoData c) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\SummaryReplicateGraphPane.cs:line 704
   at System.Linq.Enumerable.WhereListIterator`1.MoveNext()
   at System.Collections.Generic.List`1.InsertRange(Int32 index, IEnumerable`1 collection)
   at pwiz.Skyline.Controls.Graphs.SummaryReplicateGraphPane.GraphData.MakePointPairLists[TChromInfoData](DisplayTypeChrom displayType, IList`1 chromInfoResults, Func`2 isMissingValue, Func`3 createPointPair) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\SummaryReplicateGraphPane.cs:line 686
   at pwiz.Skyline.Controls.Graphs.SummaryReplicateGraphPane.GraphData.GetPointPairLists(PeptideDocNode peptideDocNode, TransitionGroupDocNode nodeGroup, DisplayTypeChrom displayType) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\SummaryReplicateGraphPane.cs:line 767
   at pwiz.Skyline.Controls.Graphs.SummaryReplicateGraphPane.GraphData.GetPeptidePointPairLists(PeptideGroupDocNode peptideGroup, PeptideDocNode nodePep, Boolean multiplePeptides) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\SummaryReplicateGraphPane.cs:line 519
   at pwiz.Skyline.Controls.Graphs.SummaryReplicateGraphPane.GraphData.InitData() in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\SummaryReplicateGraphPane.cs:line 347
   at pwiz.Skyline.Controls.Graphs.RTReplicateGraphPane.UpdateGraph(Boolean selectionChanged) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\RTReplicateGraphPane.cs:line 145
   at pwiz.Skyline.Controls.Graphs.GraphSummary.UpdateGraph(Boolean selectionChanged) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\GraphSummary.cs:line 370
   at pwiz.Skyline.Controls.Graphs.GraphSummary.UpdateUI(Boolean selectionChanged) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\Graphs\GraphSummary.cs:line 299
   at pwiz.Skyline.SkylineWindow.<UpdateRetentionTimeGraph>b__1131_0(GraphSummary g) in C:\proj\skyline_22_2\pwiz_tools\Skyline\SkylineGraphs.cs:line 3476
   at System.Collections.Generic.List`1.ForEach(Action`1 action)
   at pwiz.Skyline.SkylineWindow.UpdateSummaryGraphs() in C:\proj\skyline_22_2\pwiz_tools\Skyline\SkylineGraphs.cs:line 4582
   at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
   at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
   at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ToolStrip.WndProc(Message& m)
   at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
Exception caught at:
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.WndProcException(Exception e)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Program.cs:line 312
Nick Shulman responded:  2022-09-15 07:18
Can you send us your Skyline document?

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.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:

We saw that error a few times four years ago and I don't think we ever figured out what caused it, so it would be very helpful if we could take a look at your Skyline document.
-- Nick
sstoychev23513 responded:  2022-09-15 07:54
sure, but I'm struggling to create the .zip with share, it generates a .sky file which cannot be opened after... and share option worked fine couple of days ago...

anyway, ive uploaded all linked files so should still be able to open
Nick Shulman responded:  2022-09-15 08:12
Thank you for sending those files.
So far, I am not able to reproduce the error that you ran into.

Are you saying that you also produced a .sky file which could not be opened? If so, please send it to me (the .sky file, the, or whatever). I will figure out what Skyline did wrong.
-- Nick
sstoychev23513 responded:  2022-09-15 08:55
strange, the share produced file that cannot open is busy uploading
Nick Shulman responded:  2022-09-15 09:47
Thank you for uploading "20220914 AKI Verification Target selection All runs filtered".
That file was a .zip file and should have been named something ending with ".zip", otherwise Skyline would not know what to do with it.

After I changed the name of the file to "20220914 AKI Verification Target selection All runs filtered" I had no trouble opening it in Skyline.

I have not been able to get this error to happen. If it happens again for you, please press the "Report" button on the "Unexpected Error" dialog.
Also, please check the "Submit screenshot of Skyline window only." checkbox.

I think in this case you need to leave the "Submit skyline document" checkbox unchecked. It seems we have a bug where if the Skyline document is too large then we don't actually receive the error report at all if "Submit skyline document" was checked. I will look into fixing this.
-- Nick
sstoychev23513 responded:  2022-09-15 11:37
Thanks Nick, will do
sstoychev23513 responded:  2022-09-20 05:42
Hi Nick,

I've been getting the error message and it seems to only occur when some sort of edit is made to the Skyline document (maybe peptide removed etc) and the document is not then saved... if you still have access to my data maybe see if can replicate on your side.

Nick Shulman responded:  2022-09-20 13:32
If you send me a screenshot of what Skyline looks like when the error happens I might be able to figure out what is going on.
I'll also send you an email because it might be easier to correspond that way.
-- Nick