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, [email protected] 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
>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
