Error library-free analysis

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Error library-free analysis sstoychev  2021-05-13
 
Hi Skyline team, I get the following error when trying to do a library-free data extraction from SWATH runs. This happens at the 1st raw data conversion step, any clues to what might be causing this?:

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Skyline-daily
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Error
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OK More Info
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System.IO.IOException: Error occurred running process.

Command-line: C:\Users\6600 PROCESS\AppData\Local\Apps\2.0\NNEX7B00.JX1\W572QYT8.HKO\skyl..tion_e4141a2a22107248_0015.0000_7c1413170fdadb9e\msconvert -v --32 -z --mz5 -o "C:\Users\6600 PROCESS\AppData\Local\Temp" --outfile tcof2ros.nkp.mz5 --filter "diaUmpire params=C:\Users\6600 PROCESS\AppData\Local\Temp\4rrusmmt.q4q.params" "D:\Analyst_data\Proteomics\2021_05_05 Non TDF Cohort\Data\Hela_QC\20210503 100ng Hela_1.wiff"
Working directory:
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65
   at pwiz.Skyline.Model.DiaUmpireDdaConverter.Run(IProgressMonitor progressMonitor, IProgressStatus status) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\DiaUmpireDdaConverter.cs:line 139
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matt.chambers42 responded:  2021-05-13

Hi,

I'm still working on some occasional, hard-to-reproduce crashes in our DIA-Umpire implementation. Do you get this behavior for every run, or only sometimes? If it's every run I'll definitely need to try on your WIFF file and know what parameters you're using.

Thanks,
-Matt

 
sstoychev responded:  2021-05-13
Hi Matt,

It seems to like it's happening with all files. I now tried to re-process another .wiff which I had successfully analyzed previously with the same workflow and the same error popped up. I'm not 100% that identical settings were used but they would have been pretty close. I did do a Skyline Daliy update earlier today, not sure if that has anything to do with it:

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Skyline-daily
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Error
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OK More Info
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System.IO.IOException: Error occurred running process.

Command-line: C:\Users\6600 PROCESS\AppData\Local\Apps\2.0\NNEX7B00.JX1\W572QYT8.HKO\skyl..tion_e4141a2a22107248_0015.0000_7c1413170fdadb9e\msconvert -v --32 -z --mz5 -o "C:\Users\6600 PROCESS\AppData\Local\Temp" --outfile tsonjh1i.zjg.mz5 --filter "diaUmpire params=C:\Users\6600 PROCESS\AppData\Local\Temp\fh252pq0.3gu.params" "D:\ReSyn\DigestIF\2021_03_08\Auto HILC 3.wiff"
Working directory:
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65
   at pwiz.Skyline.Model.DiaUmpireDdaConverter.Run(IProgressMonitor progressMonitor, IProgressStatus status) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\DiaUmpireDdaConverter.cs:line 139
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