MSConvert Error
chr12is
I am having a problem with MSConvert getting my files to mzML. I
recently upgraded to TPP 4.4 from 4.3.1. The previous version of the
TPP was working fine on this system. I am running in to the same
problem on two systems, one with Windows Server 2008, and one with
Windows 7, both 64-bit systems, only one of which is running anti-
virus.
My problem is since the upgrade of the TPP, msconvert simply will not
run. I get a side by side configuration error. I have checked the
manifest for msconvert, and I have the correct visual studio files
installed for it to function. When I go to the error viewer, this is
the output that is given:
Activation context generation failed for "C:\Inetpub\tpp-bin
\msconvert.exe". Dependent Assembly
MSFileReader.XRawfile2.SxS,type="win32",version="2.1.0.20" could not
be found. Please use sxstrace.exe for detailed diagnosis.
I have tried uninstalling and reinstalling the TPP using the right
click "run as administrator" option to no avail. I am trying to
convert Waters .raw folders and I have MassLynx and ProteinLynx
installed on the systems. This is only a problem with msconvert. All
of the other binaries seem to run fine, from the ones I have tested.
Can anyone shed some light on what might be happening here?
Thanks!
Chris
Matthew Chambers
I downloaded and installed 4.4 on my development machine and I see the same issue. It's clear what the problem is though: the
MSFileReader.XRawfile2.SxS.manifest and Interop.EDAL.SxS.manifest files are not included in the installation. They must be kept side by side with the msconvert
executable. An official fix will require a TPP patch, but in the meantime, you can download these files directly from ProteoWizard and put them in your tpp-bin
directory:
http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/pwiz/utility/vendor_api/thermo/MSFileReader.XRawfile2.SxS.manifest
http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.EDAL.SxS.manifest
-Matt
chr12is
The next error I run into now when I run it is this:
###### BEGIN Command Execution ######
[Mon Aug 23 23:00:27 2010] EXECUTING: c:\Inetpub\tpp-bin\msconvert -v
--mzML -o c:/Inetpub/wwwroot/ISB/data/Chris c:/Inetpub/wwwroot/ISB/
data/Chris/ch_041810_HeLa_InGel_9_ex1.raw
OUTPUT:
format: mzML (Precision_64 [ 1000514:Precision_64
1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None)
indexed="true"
outputPath: c:/Inetpub/wwwroot/ISB/data/Chris
extension: .mzML
contactFilename:
filters:
filenames:
c:/Inetpub/wwwroot/ISB/data/Chris/ch_041810_HeLa_InGel_9_ex1.raw
processing file: c:/Inetpub/wwwroot/ISB/data/Chris/
ch_041810_HeLa_InGel_9_ex1.raw
[ReaderFail] [Reader_Waters::read()] Waters RAW reader not
implemented: support was explicitly disabled when program was built
Error processing file c:/Inetpub/wwwroot/ISB/data/Chris/
ch_041810_HeLa_InGel_9_ex1.raw
END OUTPUT
RETURN CODE:256
###### End Command Execution ######
Any idea for a workaround for this? I seem to remember being able to
convert Waters .raw folders to mzML in the old release.
Chris
On Aug 24, 10:39 am, Matthew Chambers <matt.chamber...@gmail.com>
wrote:
>
> I downloaded and installed 4.4 on my development machine and I see the same issue. It's clear what the problem is though: the
> MSFileReader.XRawfile2.SxS.manifest and Interop.EDAL.SxS.manifest files are not included in the installation. They must be kept side by side with the msconvert
> executable. An official fix will require a TPP patch, but in the meantime, you can download these files directly from ProteoWizard and put them in your tpp-bin
chr12is
support Waters at all. I guess previously I was using MassWolf to
convert to mzML. Any idea if Waters support is being programmed in to
msconvert?
Chris
Matthew Chambers
We do support Waters, but the snapshot builds have been missing it for a while due to a wipe that never got corrected. I've just sent a message about it and it
should be fixed today with a new snapshot. I let snapshot support for the old API stagnate because Waters developed a blazing fast new API for us that doesn't
require MassLynx, but the licensing issues aren't worked out yet. :(
-Matt
chr12is
information for Waters on this page:
http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Capabilities
Thats great news though, let me know when the snapshot is updated so I
can start running some files.
Thanks for the help!
Chris
On Aug 24, 11:12 am, Matthew Chambers <matt.chamber...@gmail.com>
wrote:
Matthew Chambers
The snapshot is rebuilt with Waters support (via DAC DLLs) and working with my tests:
http://teamcity.labkey.org:8080/viewLog.html?buildId=17942&tab=artifacts&buildTypeId=bt77&guest=1
Keep in mind that just like MassWolf, the pwiz Reader_Waters has no vendor peak picking for profile data. So if you want centroids from your profile data, the
only thing msconvert can do is use the very rough pwiz local maximum algorithm (which needs additional signal filtering before it works with any semblance of
sanity).
-Matt
Joe Slagel
Thanks for reporting this. As Matt said I failed to include all of the necessary components when including msconvert with the latest release of TPP 4.4.0. I'll be putting together a maintenance release shortly to address this.
-Joe
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Joe Slagel
Institute for Systems Biology
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(206) 732-1362