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Sharing .skyd error yann guitton  2023-02-23
 
Hi,

A colleague sent me a .zip file made with (File/share) from a skyline 22.2.0.351 version. when i try to open it on my computer (same version of skyline)
I have the following error. Can you give us a solution?

Best
Yann
---------------------------
Skyline
---------------------------
Failure opening C:\Users\ygu\Downloads\thermo_sd_120k.sky.
The file contains an error on line 4127 at column 8.
The isotope modification type heavy does not exist in the document settings.
---------------------------
OK More Info
---------------------------
System.Reflection.TargetInvocationException: Il existe une erreur dans le document XML (4127, 8). ---> System.InvalidOperationException: Il existe une erreur dans le document XML (4127, 8). ---> System.IO.InvalidDataException: The isotope modification type heavy does not exist in the document settings.
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadLabelType(XmlReader reader, IsotopeLabelType labelTypeDefault) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 1413
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 1328
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 1322
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 969
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 904
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 874
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 653
   à pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:ligne 617
   à pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\SrmDocument.cs:ligne 2150
   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 pwiz.Skyline.SkylineWindow.<>c__DisplayClass735_0.<OpenFile>b__0(IProgressMonitor progressMonitor) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\SkylineFiles.cs:ligne 328
   à pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 254
   --- Fin de la trace de la pile d'exception interne ---
   à pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Util\Util.cs:ligne 1965
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 202
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 140
   à pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\SkylineFiles.cs:ligne 345
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Nick Shulman responded:  2023-02-23
If you send us the file "thermo_sd_120k.sky" we will be able to send you back a fixed version of the file that you will be able to open.

If that file is less than 50MB you can attach it to this support request. If it is larger than that you can upload it here:
https://skyline.ms/files.url

Skyline has had some bugs where if you remove or change an isotope label type at "Settings > Peptide Settings > Modifications" you could get yourself in a state where you could save the document but not open it afterwards.

--Nick
 
yann guitton responded:  2023-02-23
Hi Nick,

The file sky.zip is big 1.5 Go can you download it from a link (https://nextcloud.inrae.fr/s/jzDsCNGdr4SBQNr) ?

Best
Yann
 
Nick Shulman responded:  2023-02-23
I don't think the .sky.zip that you pointed me at has any error in it.
I believe that if you were to open that .sky.zip file in Skyline it would probably succeed, and you not get the error that you originally posted about.

I am pretty sure that the "thermo_sd_120k.sky" that you failed to open is different than the file that is inside of the .sky.zip.

If you send me the "thermo_sd_120k.sky" that you are having trouble with, I can fix it for you. Alternatively, I believe that you could open the .sky.zip file without error.
(I can't actually open that .sky.zip file in Skyline right now because I only have a slow internet connection right now but I was able to look at the .sky file in there and it does not appear that it could produce the error message that you posted).
-- Nick
 
yann guitton responded:  2023-02-23
I'm really sorry but when I try to :
1- open Skyline and then 2- File/Open... and then 3- choose the .sky.zip I have an other error

I will ask my colleague to build a smaller sky.zip file and try again

Best
Yann

---------------------------
Skyline
---------------------------
Failure extracting Skyline document from zip file C:\Users\ygu\Downloads\thermo_sd_120k.sky.zip.
Cannot read that as a ZipFile
---------------------------
OK More Info
---------------------------
System.Reflection.TargetInvocationException: Cannot read that as a ZipFile ---> Ionic.Zip.ZipException: Cannot read that as a ZipFile ---> Ionic.Zip.BadReadException: Could not read block - no data! (position 0x61914CD6)
   à Ionic.Zip.SharedUtilities._ReadFourBytes(Stream s, String message)
   à Ionic.Zip.ZipEntry.HandleUnexpectedDataDescriptor(ZipEntry entry)
   à Ionic.Zip.ZipEntry.ReadEntry(ZipContainer zc, Boolean first)
   à Ionic.Zip.ZipFile.ReadIntoInstance_Orig(ZipFile zf)
   à Ionic.Zip.ZipFile.ReadIntoInstance(ZipFile zf)
   --- Fin de la trace de la pile d'exception interne ---
   à Ionic.Zip.ZipFile.ReadIntoInstance(ZipFile zf)
   à Ionic.Zip.ZipFile.Read(String fileName, TextWriter statusMessageWriter, Encoding encoding, EventHandler`1 readProgress)
   à pwiz.Skyline.Model.SrmDocumentSharing.Extract(IProgressMonitor progressMonitor) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\SrmDocumentSharing.cs:ligne 88
   à pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 254
   --- Fin de la trace de la pile d'exception interne ---
   à pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Util\Util.cs:ligne 1965
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 202
   à pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:ligne 140
   à pwiz.Skyline.SkylineWindow.OpenSharedFile(String zipPath, FormEx parentWindow) dans C:\proj\skyline_22_2\pwiz_tools\Skyline\SkylineFiles.cs:ligne 226
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Nick Shulman responded:  2023-02-23
This new error is the error that you get if Skyline thinks you are trying to open a .zip file but it is not a real .zip file. This most often happens if a file has been inappropriately renamed.
--Nick
 
yann guitton responded:  2023-02-23
Hi Nick,

With a smaller file it works now. Maybe more an issue on the big file transfer between me and my colleague than a Skyline issue

Best