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 On Wed, Jul 12, 2017 at 9:10 AM, David Shteynberg < [email protected]> wrote: > The mzML and the pepXML is the minimum I would need to test the issue. > Thanks! > > -David > > On Wed, Jul 12, 2017 at 9:04 AM, Jason Winget <[email protected]> wrote: > >> 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 <[email protected]> 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* >>>> >>>> >>>> -- >>>> 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. >>>> >>> >>> -- >> 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. >> > > -- 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.
