Interesting error: TIMSTOF and Mascot

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Interesting error: TIMSTOF and Mascot Jason Held  2020-06-12
 

Hi,

I'm trying to build a library from TIMSTOF data search with mascot. I'm using the DAT files to build the library and getting this error:

System.IO.IOException: ERROR: Maximum limit of 2000 spectrum source files was exceeded. There was most likely a problem reading the filenames.
ERROR:
ERROR: reading file F013408.dat
ERROR: Maximum limit of 2000 spectrum source files was exceeded. There was most likely a problem reading the filenames.
ERROR:
ERROR: reading file F013416.dat

Command-line: C:\Users\lab_held.pcl-held1\AppData\Local\Apps\2.0\NRM38HKN.2B5\OM37C28G.N7K\skyl..tion_e4141a2a22107248_0014.0001_1e739a267632795e\BlibBuild -s -A -H -o -c 0.99 -i Bowman005_TIMSTOF -S "C:\Users\lab_held.pcl-held1\AppData\Local\Temp\tmp2696.tmp" "C:\Skyline\SpectralLibraries\Bowman005_TIMSTOF.redundant.blib"
Working directory: S:\Users\Jason\Bowman005-New2CysMutantForPaperTIMSTOF
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Mode\Lib\BiblioSpecLiteBuilder.cs:line 155

Cheers,
Jason

 
 
Brendan MacLean responded:  2020-06-17

Hi Jason,
We'll need to take a look at your .dat file. This indicates that we are having trouble parsing the source file name where we expect it to be. I assume you don't really expect F013416.dat to contain search results for over 2000 runs.

If you could upload an example file that causes this error to:

https://skyline.ms/files.url

One of the BlibBuild developers will have a look and figure out why our code is getting confused.

Thanks for reporting it.

--Brendan

 
Jason Held responded:  2020-06-19

Thanks Brendan. F013408.dat that led to the error has been uploaded to your location.

Nope, I certainly don't expect the dat file to have search results from 2000 runs ;).

Jason

 
matt.chambers42 responded:  2020-06-22

It'll be fixed in the next daily. This Mascot DAT file uses tildes (~) for quoting filenames, something we hadn't encountered before. Is there anything particular about the Mascot installation that created it? Non-US regional settings perhaps?

 
Jason Held responded:  2020-06-22

Thanks Brendan. Nothing special with regard to my mascot installation that I know of, but it is the first time I'm dealing with Bruker TIMSTOF data and their MGF outputs.