trapper fails when large files processed

[Ilya.Agron]

There's a question about the trapper in TPP (Win-version).
Now we use trapper to convert .d (Agilent-files, Q-ToF) in mzXML; and
then use Decon2ls to process it into deconvoluted and deisotoped data
for AMT approach. It's our work flow very shortly.
There's problem, that we can't process with trapper large files (as
our 4.5 Gb chromatograms). It fails during the processing. Is it the
problem of the memory?
May you advise something to solve this problem?
Thanks in advance!

[David Shteynberg]

Hello Ilya,

I have not used trapper but in a situation like this a more detailed
description of the failure may be needed. Are there any error
messages produced? What is the system you are running trapper on?
What else have to tried to address this issue? Can you post a problem
file to Tranche and share the key so we can try to reproduce the
problem here?

-David

[Ilya.Agron]

Hello.

The last time I've used it the error looked this way:

E:\trapper>trapper.exe --mzXML -c E:\trapper\MasKate1-r001.d
single mode file
(got computer name: RIGHT)
ERROR at .\MHDACWrapper.cpp, 227:
HR = -2147024882
error getting spectrum
empty scan object

E:\trapper>

What could it be?
May be, it's not memory problem. There's Windows OS.

What's Tranche? Is it free upload resource?
Sure, I can and want to upload it.

Thanks!

On Jul 7, 8:16 pm, David Shteynberg <dshteynb...@systemsbiology.org>
wrote:

> Hello Ilya,
>
> I have not used trapper but in a situation like this a more detailed
> description of the failure may be needed.  Are there any error
> messages produced? What is the system you are running trapper on?
> What else have to tried to address this issue?  Can you post a problem
> file to Tranche and share the key so we can try to reproduce the
> problem here?
>
> -David
>

> On Thu, Jul 2, 2009 at 12:26 AM, Ilya.Agron<ilya.ag...@gmail.com> wrote:
>
> > There's a question about the trapper in TPP (Win-version).
> > Now we use trapper to convert .d (Agilent-files, Q-ToF) in mzXML; and
> > then use Decon2ls to process it into deconvoluted and deisotoped data
> > for AMT approach. It's our work flow very shortly.
> > There's problem, that we can't process with trapper large files (as

> > our4.5Gbchromatograms). It fails during the processing. Is it the

[David Shteynberg]

Hello Ilya,

The error explains the problem "error getting spectrum
empty scan object". The error is referring to the follow bit of
code:

215 MH::BDA::IBDASpecData* MHDACWrapper::GetSpectrum
(MH::IMsdrDataReader* pMSDataReader,
216 double retentionTime,
217 MH::MSScanType scanType,
218 MH::IonPolarity ionPolarity,
219 MH::IonizationMode ionizationMode,
220 MH::IMsdrPeakFilter* filter,
221 VARIANT_BOOL* filterOnCentroid)
222 {
223 MH::BDA::IBDASpecData* specData = NULL;
224 COMCHECK(pMSDataReader->GetSpectrum_7(
225 retentionTime,
226 scanType,
227 ionPolarity,
228 ionizationMode,
229 filter,
230 *filterOnCentroid,
231 &specData),
232 "error getting spectrum");
233
234 return specData;
235 }

The failure is on a COM object call to an Agilent software library
function call. Are you sure there is actual data in the file you are
giving to trapper to convert? Have you opened this data file in an
agilent viewer? Would you mind posting your raw data to our FTP site
(instructions here
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F)?
We can then try to reproduce your problem in a debugger to find the
cause of failure.

-David