Issue 648: Error when building a library from MetaMorpheus results (*.mzID)

Status:resolved
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:3
Milestone:4.3
Opened:2019-05-21 by Yishai
Changed:2019-06-21 by matt.chambers42
Resolved:2019-06-21 by matt.chambers42
Resolution:Fixed
Closed:
2019-05-21 Yishai
Title»Error when building a library from MetaMorpheus results (*.mzID)
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»4.3
Hi,
I tried building a library from MetaMorpheus search results (*.mzID file) and got this error:
System.IO.IOException: ERROR: Unknown input file type 'HF2_9387_YLE_hela_110419_1_F1a_2_110419-calib.mzID'.

   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 137

Skyline version is 4.2.0.19072.

Thanks,

Yishai

2019-05-21 Brendan MacLean
Assigned ToBrendan MacLean»matt.chambers42@gmail.com
Interesting. I would have expected the library builder to know the file type .mzid but perhaps complain about an unknown score type.

We probably need an example of this type of .mzID file and whatever spectrum file type you are expecting the spectral library builder to get the spectra from, since mzIdentML does not contain spectra. Usually, this would be MGF or mzML, or perhaps the raw data file(s), if MetaMorpheus reads those without requiring conversion to MGF or mzML.

2019-05-21 matt.chambers42
Try renaming the extension to lowercase .mzid. The culprit is probably some Linux-centric logic in BiblioSpec where the filesystem IS case-sensitive.

2019-05-22 Brendan MacLean
Let's fix that logic to be case insensitive on the file extension.

Yishai responded in email:

I changed the mzID to mzid and now it says there are no spectra. Also tried changing mzML to mzml.

System.IO.IOException: ERROR: No spectra were found for the new library.

   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 137

================end email========================

Are the .mzid and .mzML (usually capitalized like this) in the same directory? It may be that the library builder is having trouble finding the mzML, but I would expect it to give an error about not being able to find a file rather than not having any spectra.

Matt may still need to get your files, which you can upload to:

https://skyline.ms/files.url

2019-05-24 matt.chambers42
This appears to be a bug with MetaMorpheus's spectrum ids. The spectrum ids in the mzML file are correct Thermo ids: "controllerType=1 controllerNumber=0 scan=1234". The spectrum ids in the mzIdentML file are not correct Thermo ids: "scan=1234". BiblioSpec could do a better job informing the user about this problem though. I will fix that. The MM bug can be reported at: https://github.com/smith-chem-wisc/MetaMorpheus/issues

2019-05-24 matt.chambers42
Oops, that should be "controllerType=0 controllerNumber=1 scan=1234"

2019-06-21 matt.chambers42
resolve as Fixed
Statusopen»resolved
Assigned ToGuest»matt.chambers42@gmail.com
The next Skyline daily will include a BiblioSpec which will give a sensible warning message when the mzIdentML nativeID format differs from the mzML nativeID format. Thanks for reporting the bug to MetaMorpheus: it looks like they're working on fixing it.