Library build error (dat file)

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Library build error (dat file) Jason Held  2019-02-14
 

I'm trying to build a library from a large mascot .dat file (2.2 GB) and getting: ERROR unable to read filesize of (my filename).dat.

More info pasted below. Error screenshot attached.

Cheers,
Jason

System.IO.IOException: ERROR: Unable to read filesize of F011061_Cys_NewRat_PlusRED_0p0232.dat.
ERROR:

Command-line: C:\Users\lab_held.pcl-held1\AppData\Local\Apps\2.0\NRM38HKN.2B5\OM37C28G.N7K\skyl..tion_e4141a2a22107248_0004.0002_ed14b445d33623de\BlibBuild -s -A -H -o -c 0.9768 -i GloCys055_Cys_PlusRED_Mascot_0p023 "C:\Skyline\SpectralLibraries\GloCys055_Cys_PlusRED_Mascot_0p023.redundant.blib"
Working directory: S:\Users\Jason\GloCys055_131231\Cys
Standard input:
F011061_Cys_NewRat_PlusRED_0p0232.dat

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 60
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in C:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 178
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 144

 
 
Brian Pratt responded:  2019-02-14
Hi Jason,

Could you zip that .dat file and upload to http://skyline.ms/files.url ? I'd like to investigate.

Thanks

Brian Pratt
 
Jason Held responded:  2019-02-14
Done, thanks
Jason
 
Brendan MacLean responded:  2019-02-14
Hi Jason,
So, is S:\Users a network drive? If so, there may be some kind of issue with it and you may have better success copying your .dat file to a local disk drive. Also, if so, I doubt Brian will have much success in reproducing the issue. Failing to get the file size of the .dat file sounds pretty basic to me. Though, I expect it is the Mascot DAT reader library causing the failure, since I can't imagine why BlibBuild itself would be performing this operation.

--Brendan
 
Jason Held responded:  2019-02-14
Bendan-

S: is a network drive, but I've used it to make libraries from dat files many times. Also, I moved the dat file to the C: drive, tried to make a library, and get the same error (below). I think its something about this dat file specifically...

Cheers
Jason

System.IO.IOException: ERROR: Unable to read filesize of F011061_Cys_NewRat_PlusRED_0p0232.dat.
ERROR:

Command-line: C:\Users\lab_held.pcl-held1\AppData\Local\Apps\2.0\NRM38HKN.2B5\OM37C28G.N7K\skyl..tion_e4141a2a22107248_0004.0002_ed14b445d33623de\BlibBuild -s -A -H -o -c 0.99 -i test "C:\Skyline\SpectralLibraries\test.redundant.blib"
Working directory: C:\Users\Jason
Standard input:
F011061_Cys_NewRat_PlusRED_0p0232.dat

   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 60
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in C:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 178
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 144
 
Brendan MacLean responded:  2019-02-14
Okay, then we should be able to reproduce the problem here. Though, we may end up sending it to Matrix Science for .dat forensics. Thanks for the clarification.
 
shannon holt responded:  2019-04-23
Hi There,

I was just wondering if the problem with this error was found. As I am getting the same error: unable to read filesize.

Thanks,
Shannon
 
Nick Shulman responded:  2019-04-23
This error is happening because the file is more than 2GB in size.
This is a bug in BiblioSpec which should be straightforward for us to fix.

Sorry that we seem to have forgotten about this bug, and thank you for reminding us.
-- Nick
 
shannon holt responded:  2019-05-06
Hi Nick,

Thanks for the quick response. Is there an estimated date for when you think this might be fixed? Sorry for bugging you, I just have an experiment running in a couple of weeks I'm trying to organise.

Cheers,
Shannon
 
Nick Shulman responded:  2019-05-06
This will be fixed in the next update of Skyline-Daily, which happen every few weeks or so.

This bug was incidentally fixed (on April 23) as a part of other work that was done in terms of making sure the BiblioSpec would work with filenames that contained non-english characters.

I believe this bug has been fixed in the latest Skyline Administrator Installer if you can't wait for the next regular Skyline-Daily.

https://skyline.ms/wiki/home/software/Skyline/daily/page.view?name=install-administrator-64
--Nick
 
shannon holt responded:  2019-05-07
Awesome. Thanks very much :)
 
Brian Pratt responded:  2019-05-07
Hi Shannon,

As the fix is already in our codebase, you can actually have a revised BiblioSpec build right now:

https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=Download%20and%20build

Look for the "Pre-compiled binaries" section at the bottom of the page.

Best Regards,

Brian Pratt
 
shannon holt responded:  2019-05-09
HI

I get errors when running exec files in this bibilio spec.. Please refer to the attched screenshot..can you please send me the steps to follow once I have downloaded this folder.

Regards
 
Brian Pratt responded:  2019-05-09
It's probably just that you didn't unzip to the location where bibliospec is already installed. That download isn't a proper installer, it assumes you're updating an existing installation.

Best Regards,

Brian
 
Brendan MacLean responded:  2019-05-09
If you have a normal web installation of Skyline, you can use the steps described in the "Recovering from a Broken Installation" tip to find your Skyline.exe or Skyline-daily.exe or BlibBuild.exe and put the replacement there. You probably also need to right-click on the BilbBuild.exe and BlibFilter.exe, click properties and check Unblock on this files, since Windows will block them if they were downloaded with a ZIP file and unzipped.

... Or you could just wait for the next Skyline-daily, which I will try to get out by Monday.
 
shannon holt responded:  2019-05-10
Great, thanks so much for your help!!