PTMProphet Problems in TPP 5.0.0

[Magnus....@gmail.com]

Hey guys,

Great work with the new TPP version! However, we are having issues with PTMProphet in TPP 5.0.0 (TPP v5.0.0 Typhoon, Build 201610111222-7423 (Windows_NT-x86_64). Regardless of the data I try (iProphet files from PeptideProphet files from Comet or X!Tandem phosphopeptide identifications from ETD data), PTMProphet crashes with the following error message:

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.

Command FAILED
RETURN CODE:65280

On the command line, I get:

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'
  what():  failed opening file: The system cannot find the file specified.
: iostream error


The PeptideProphet and iProphet results look reasonable (plenty of both phospho and non-phospho peptides identified with high probabilities from good looking spectra)

Has anyone else seen the same problem?


Best regards,

Magnus Palmblad

[David Shteynberg]

Hi Magnus,

From the error message it seems like it is failing in boost because one of the input pepXML files or the internally referenced mzML/mzXML data files cannot be found in the path specified.  Can you check the paths of the mzML files  and make sure they are accessible and readable.   How are you running PTMProphet on the commandline?

Thanks,

-David

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[Veit Schwaemmle]

Hi guys!

I think we nailed the problem down to two issues:

a) Empty lines in the pep.xml files lead to a segmentation fault in PTMProphetParser. This can be fixed by substituting
    data = strstr(nextline, "<");
     while(data != NULL)  {
by
    while(data != NULL && data != "") {
      data = strstr(nextline, "<");
in line 250 of PTMProphetParser.cpp.

b) When applying PTM prophet on spectra searched without fixed modification on Cys, also a segmentation fault appears. There are no values assigned to unmodified Cys but only to modified ones in the Peptide class of SpectraST (called from PTM prophet):

Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C[160]"] = new double[2];
Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C[160]"][0] = 133.04360;
Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C[160]"][1] = 0.0;

This can be fixed by adding a few lines to cover AAMonoisotopicImmoniumTable)["C"] such as
Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C"] = new double[2];
Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C"][0] = ???;
Peptide.cpp:  (*AAMonoisotopicImmoniumTable)["C]"][1] = ???;

Best regards
Veit

[David Shteynberg]

Thanks for this.  We will correct the problems.

Cheers,

-David

--

[Veit Schwaemmle]

Hi David,

I just posted some explanation where the error came from but cannot see the post anymore. Did you get it?

Best regards
Veit

On Friday, 14 October 2016 18:10:52 UTC+2, David Shteynberg wrote:

Hi Magnus,

From the error message it seems like it is failing in boost because one of the input pepXML files or the internally referenced mzML/mzXML data files cannot be found in the path specified.  Can you check the paths of the mzML files  and make sure they are accessible and readable.   How are you running PTMProphet on the commandline?

Thanks,

-David

On Fri, Oct 14, 2016 at 5:38 AM, Magnus....@gmail.com <Magnus....@gmail.com> wrote:

Hey guys,

Great work with the new TPP version! However, we are having issues with PTMProphet in TPP 5.0.0 (TPP v5.0.0 Typhoon, Build 201610111222-7423 (Windows_NT-x86_64). Regardless of the data I try (iProphet files from PeptideProphet files from Comet or X!Tandem phosphopeptide identifications from ETD data), PTMProphet crashes with the following error message:

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.

Command FAILED
RETURN CODE:65280

On the command line, I get:

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'
  what():  failed opening file: The system cannot find the file specified.
: iostream error


The PeptideProphet and iProphet results look reasonable (plenty of both phospho and non-phospho peptides identified with high probabilities from good looking spectra)

Has anyone else seen the same problem?


Best regards,

Magnus Palmblad

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[Jason Winget]

I think some of these issues are lingering.

Using TPP 5.0.0, when I run PTMProphet via Petunia, it will read the files and go through "iterating PTM model" etc, however I get no output written to the directory or the original pepXML files.

If I copy the command from Petunia or enter it manually on the command line, I either get the same "failed opening file" error or an "unrecognized mod token" error. I have tried rearranging the arguments a few different ways without success.

I then upgraded to TPP 5.0.1 from Sourceforge and now I get a boost error even in Petunia (likely the same "failed opening file" error) and the "unrecognized mod token" error on the command line.

For reference my command line (on Windows) is as follows:

PTMProphetParser.exe NQR:0.984016,M:15.9949:-63.998286:-81.024835:-82.008850,STY:79.966331:-97.97690:-115.9880,K:114.042927 MZTOL=0.1 PPMTOL=1 .\interact.pep.xml .\interact.ptm.pep.xml

[David Shteynberg]

Hi Jason,

I am not sure what is going on here and without having the data it would be difficult to pinpoint.  Are you able to put together a dataset that I can use to reproduce the bug and troubleshoot?

Thanks,

-David

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[Jason Winget]

Sure I can do that.

How far back do you need - mzML, pep.xml search results, something else?

On Wednesday, July 12, 2017 at 11:02:50 AM UTC-4, David Shteynberg wrote:

Hi Jason,

I am not sure what is going on here and without having the data it would be difficult to pinpoint.  Are you able to put together a dataset that I can use to reproduce the bug and troubleshoot?

Thanks,

-David

On Wed, Jul 12, 2017 at 5:30 AM, Jason Winget <jwi...@gmail.com> wrote:

I think some of these issues are lingering.

Using TPP 5.0.0, when I run PTMProphet via Petunia, it will read the files and go through "iterating PTM model" etc, however I get no output written to the directory or the original pepXML files.

If I copy the command from Petunia or enter it manually on the command line, I either get the same "failed opening file" error or an "unrecognized mod token" error. I have tried rearranging the arguments a few different ways without success.

I then upgraded to TPP 5.0.1 from Sourceforge and now I get a boost error even in Petunia (likely the same "failed opening file" error) and the "unrecognized mod token" error on the command line.

For reference my command line (on Windows) is as follows:

PTMProphetParser.exe NQR:0.984016,M:15.9949:-63.998286:-81.024835:-82.008850,STY:79.966331:-97.97690:-115.9880,K:114.042927 MZTOL=0.1 PPMTOL=1 .\interact.pep.xml .\interact.ptm.pep.xml

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[David Shteynberg]

The mzML and the pepXML is the minimum I would need to test the issue.  Thanks!

-David

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[David Shteynberg]

Hi Jason,

This issue has been solved in the latest version of my code that I compiled here:

https://www.dropbox.com/s/c8o6i6yqe6h33u4/PTMProphetParser.exe?dl=0

You can replace your current binary in c:\TPP\bin (or where you installed the TPP).

Cheers,

-David