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* -- 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.
