Failure opening ...\...sky - error on line X at column Y

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Failure opening ...\...sky - error on line X at column Y vogelw  2017-04-21
 
Hello,
Any thoughts on how I can recover from this error ?

Screen shot of ther error message attached: "The file contains an error on line X at column9

The XML section ending at that line is also attached.
      <precursor

....

      </precursor> # the line referred to in the error message

Nothing that I can see therein.

Cheers,
Walter
 
 
Nick Shulman responded:  2017-04-21
Can you press the "More Info" on that message box, and tell us what it says? (You should just be able to select the text of the stack trace and copy/paste it into your response).

In this case, I think you have discovered a bug in Skyline, and 44989 is the line that Skyline was on when the bug manifested itself.
 
vogelw responded:  2017-04-21
Sorry the detailed error message:


System.Reflection.TargetInvocationException: There is an error in XML document (44989, 9). ---> System.InvalidOperationException: There is an error in XML document (44989, 9). ---> System.IndexOutOfRangeException: Precursor isotope [M+2] is outside the isotope distribution -1 to 1.
   at pwiz.Skyline.Model.SequenceMassCalc.GetFragmentMass(String seq, IonType type, Int32 ordinal, Nullable`1 decoyMassShift, Int32 massIndex, IsotopeDistInfo isotopeDists, ExplicitSequenceMods mods) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SequenceUtil.cs:line 1042
   at pwiz.Skyline.Model.SequenceMassCalc.GetFragmentMass(Transition transition, IsotopeDistInfo isotopeDist, ExplicitSequenceMods mods) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SequenceUtil.cs:line 1008
   at pwiz.Skyline.Model.SrmDocument.ReadTransitionXml(XmlReader reader, XmlReadContext context, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2843
   at pwiz.Skyline.Model.SrmDocument.ReadTransitionListXml(XmlReader reader, XmlReadContext context, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2789
   at pwiz.Skyline.Model.SrmDocument.ReadTransitionGroupXml(XmlReader reader, XmlReadContext context, Peptide peptide, ExplicitMods mods, DocNodeCustomIon customIon) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2596
   at pwiz.Skyline.Model.SrmDocument.ReadTransitionGroupListXml(XmlReader reader, XmlReadContext context, Peptide peptide, ExplicitMods mods, DocNodeCustomIon customIon) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2517
   at pwiz.Skyline.Model.SrmDocument.ReadPeptideXml(XmlReader reader, XmlReadContext context, PeptideGroup group, Boolean isCustomMolecule) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2339
   at pwiz.Skyline.Model.SrmDocument.ReadPeptideListXml(XmlReader reader, XmlReadContext context, PeptideGroup group) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2255
   at pwiz.Skyline.Model.SrmDocument.ReadProteinXml(XmlReader reader, XmlReadContext context) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2147
   at pwiz.Skyline.Model.SrmDocument.ReadPeptideGroupListXml(XmlReader reader, XmlReadContext context) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2062
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2016
   at System.Xml.Serialization.XmlSerializationReader.ReadSerializable(IXmlSerializable serializable, Boolean wrappedAny)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderSrmDocument.Read1_srm_settings()
   --- End of inner exception stack trace ---
   at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass121.<OpenFile>b__11f(IProgressMonitor progressMonitor) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 255
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 228
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 179
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 130
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 259
 
Nick Shulman responded:  2017-04-21
I have never seen that error before.
Can you send us your entire .sky file?
If it is less than 50MB, you can attach it to this message.

I will also send you an email with alternative ways of sending us files.
 
Nick Shulman responded:  2017-04-21
Thank you for sending me your Skyline document.
It turns out that we have seen this error before:
https://skyline.ms/announcements/home/support/thread.view?entityId=f9de728b-016e-1034-b62a-da202582f7dc

This happens if your peptide contains sulfur (i.e. methionine) and you have too high of a resolution specified for the resolving power of the instrument on:
Settings > Transition Settings > Full Scan > MS1 filtering > Resolving Power

You can work around this issue and make it possible to open your Skyline document by opening the .sky file in a text editor.

On line 38, where it says:
precursor_res="400000"
change that to a lower number, such as "200000".

Sorry about this bug. I will try to fix this soon.
 
vogelw responded:  2017-04-21
That worked.
Thanks

Walter
 
camille illiano responded:  2019-07-05
Hi,
I have some issues while opening some skyline files.
Here the error I have for several files (different raw files)
---------------------------
Skyline
---------------------------
Failure opening //tn02.genome.ulaval.ca\proteomique\resultats\RD\RD120_Altis\RD120_HeLa\RD120_testHeLa_190704Sched_2.sky.
The file contains an error on line 165 at column 12.
No modification named Label:18O(1) (C-term) was found in this document.
---------------------------
OK More Info
---------------------------
System.Reflection.TargetInvocationException: Il existe une erreur dans le document XML (165, 12). ---> System.InvalidOperationException: Il existe une erreur dans le document XML (165, 12). ---> System.IO.InvalidDataException: No modification named Label:18O(1) (C-term) was found in this document.
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadExplicitMods(XmlReader reader, String name, String nameElMod, Peptide peptide, IsotopeLabelType labelTypeDefault) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 1014
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadExplicitMods(XmlReader reader, Peptide peptide) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 971
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 869
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 761
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 732
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 573
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 539
   à pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:ligne 2022
   à System.Xml.Serialization.XmlSerializationReader.ReadSerializable(IXmlSerializable serializable, Boolean wrappedAny)
   à Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderSrmDocument.Read1_srm_settings()
   --- Fin de la trace de la pile d'exception interne ---
   à System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
   à System.Xml.Serialization.XmlSerializer.Deserialize(TextReader textReader)
   à pwiz.Skyline.SkylineWindow.<>c__DisplayClass925_0.<OpenFile>b__0(IProgressMonitor progressMonitor) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:ligne 301
   à pwiz.Skyline.Util.ProgressWaitBroker.PerformWork(ILongWaitBroker broker) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\UtilUI.cs:ligne 123
   à pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 232
   --- Fin de la trace de la pile d'exception interne ---
   à pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\Util.cs:ligne 1854
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 180
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 132
   à pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) dans C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:ligne 295
---------------------------

Here is two skyline file, I don't know where the difference between them and why I can open one of them and why I can't open the other one...
RD120_testHeLa_190704Sched_3.sky : file that doesn't work
RD120_testHeLa190703nonSched.sky : this file is working



Thanks for your help

Camille
 
Brian Pratt responded:  2019-07-05
It appears that you somehow removed a heavy modification from your peptide settings while it was still in use.

If you open RD120_testHeLa_190704Sched_3.sky in a text editor and replace the line

        <heavy_modifications />

with these lines

        <heavy_modifications>
          <static_modification name="Label:18O(1) (C-term)" terminus="C" formula="O' - O" unimod_id="258" short_name="Ob1" />
        </heavy_modifications>

it should be OK again.

Thanks for using the Skyline support board!

Brian Pratt
 
Brendan MacLean responded:  2019-07-05
Skyline, however, shouldn't be writing out a .sky file like this with an internal inconsistency that causes it to fail to load. If you can figure out the steps you took to get into the state where Skyline saved an inconsistent .sky file, we would be very interested in knowing those steps, so that we can fix Skyline to prevent that case.

I tried a few things myself, but haven't been able to cause this issue.

Thanks for reporting it.

--Brendan
 
camille illiano responded:  2019-07-05
Instead of modifiying every text file like you suggested Brian, I started over and I realize that, for no reason when I create a new skyline file, I have in peptides settings parameters 'Label:18O(1) (C-term)' that is added
settings >peptides settings >modifications >isotope modifications 'Label:18O(1) (C-term)'

So I had to remove it and this works!

I am investigating to find where does this come from and I will report it to you (if I find the issue)

Thanks a lot for your answers !