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Error importing DIA-NN search results with newest Skyline-daily update

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Error importing DIA-NN search results with newest Skyline-daily update Shawn Rice  2024-05-13 06:40
 
Greetings,
After updating Skyline-daily, I have not been able to read search results for DIA-NN. This includes search results that have previously been imported into Skyline, so the results files should be fine. The version of DIA-NN is the same that has previously allowed for the successfully imported into Skyline. The error message is copied below.

Thanks,
Shawn

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ERROR: could not find precursorId 'AVGVPALGFSPMNR2' in speclib; is 'enolase.report.tsv' the correct report TSV file?
ERROR: reading file enolase.report.lib.tsv.speclib

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\LC9H788V.2T0\ENRYOW2B.Y1Z\skyl..tion_9286511f3362df93_0017.0001_7a74d73c81fd676c\BlibBuild -s -A -H -v warn -o -c 0.95 -i skyline -S "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant202405130929.stdin.txt" "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant.blib"
Working directory: E:\Belani_240509\enolase
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OK More Info
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System.IO.IOException: ERROR: could not find precursorId 'AVGVPALGFSPMNR2' in speclib; is 'enolase.report.tsv' the correct report TSV file?
ERROR: reading file enolase.report.lib.tsv.speclib

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\LC9H788V.2T0\ENRYOW2B.Y1Z\skyl..tion_9286511f3362df93_0017.0001_7a74d73c81fd676c\BlibBuild -s -A -H -v warn -o -c 0.95 -i skyline -S "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant202405130929.stdin.txt" "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant.blib"
Working directory: E:\Belani_240509\enolase ---> System.IO.IOException: ERROR: could not find precursorId 'AVGVPALGFSPMNR2' in speclib; is 'enolase.report.tsv' the correct report TSV file?
ERROR: reading file enolase.report.lib.tsv.speclib

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\LC9H788V.2T0\ENRYOW2B.Y1Z\skyl..tion_9286511f3362df93_0017.0001_7a74d73c81fd676c\BlibBuild -s -A -H -v warn -o -c 0.95 -i skyline -S "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant202405130929.stdin.txt" "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant.blib"
Working directory: E:\Belani_240509\enolase

Output:
Reading results from enolase.report.lib.tsv.speclib.
ERROR: could not find precursorId 'AVGVPALGFSPMNR2' in speclib; is 'enolase.report.tsv' the correct report TSV file?
ERROR: reading file enolase.report.lib.tsv.speclib
100%

 ---> System.IO.IOException: ERROR: could not find precursorId 'AVGVPALGFSPMNR2' in speclib; is 'enolase.report.tsv' the correct report TSV file?
ERROR: reading file enolase.report.lib.tsv.speclib

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\LC9H788V.2T0\ENRYOW2B.Y1Z\skyl..tion_9286511f3362df93_0017.0001_7a74d73c81fd676c\BlibBuild -s -A -H -v warn -o -c 0.95 -i skyline -S "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant202405130929.stdin.txt" "E:\Belani_240509\Exp._Control_Enolase\skyline.redundant.blib"
Working directory: E:\Belani_240509\enolase
   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.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 433
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161
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Nick Shulman responded:  2024-05-13 07:39
I do not know the answer to your question but if you send us your files we might be able to figure it out.

I am not sure which files we would need so it might be best if you could send us all of the files that are in the same folder as your .speclib file.
You can zip everything up and upload it here:
https://skyline.ms/files.url

By the way, if you ever want to run an older version of Skyline-daily you can download the appropriate .zip file from here:
https://skyline.ms/filecontent/home/software/Skyline/daily/begin.view

The not-quite-most-recent version of Skyline-daily would be this one here:
https://skyline.ms/_webdav/home/software/Skyline/daily/%40files/Skyline-daily-64_23_1_1_418.zip

After you have downloaded this .zip file, you might need to "unblock" it by right-clicking on it in Windows Explorer, choosing "Properties" and then checking the "unblock" checkbox.
Then you can unzip the file and run "Skyline-daily.exe" in a subfolder of the unzipped files.

I don't think much has changed in the area of reading DIA-NN search results in the past few months, but back in December some things did change.
After we see your files we will probably be able to figure out what is going on.
-- Nick
 
Shawn Rice responded:  2024-05-13 10:27
Thanks for the information. I have uploaded the DIA-NN results folder to the uploads folder, enolase.zip.

Thanks Again,
Shawn
 
Matt Chambers responded:  2024-05-13 10:39
The date modified times are suspicious here. The speclib has a modified time ~20m AFTER the report TSV. Since the speclib is (AFAIK) used to generate the report, that almost certainly means the report is stale and needs to be regenerated. Which would explain the precursorId mismatch between report and speclib.