Thanks for this. We will correct the problems.
Cheers,
-David
On Fri, Oct 14, 2016 at 9:14 AM, Veit Schwaemmle <veitv...@gmail.com> wrote:
> 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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