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 


On Friday, 14 October 2016 14:38:55 UTC+2, 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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