Hi Felipe, Thanks for sharing your problem with me. I was able to implement a fix for this issue and I can provide you with a file to test. Are you running this analysis on windows or linux?
Cheers, -David On Tue, Mar 19, 2019 at 12:17 PM David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Dear Felipe, > > Much has changed in PTMProphet, with an emphasis on known PTM > localizations. These changes seem to have broken the MASSDIFFMODE of > PTMProphet as you have observed. I would be happy to help track down the > issue, but I could use your help in providing the repro. Please let me > know if you can post your dataset for me to troubleshoot. Meanwhile, > please use the older version that has a functional MASSDIFFMODE. > > Thanks! > -David > > On Tue, Mar 19, 2019 at 10:55 AM Felipe da Veiga Leprevost < > leprevos...@gmail.com> wrote: > >> Hi; >> >> I'm getting an error when running PTMProphet 5.2.0. using MSFragger open >> search results and using the MASSDIFFMODE option. Without the option the >> program is able to finish without problems (same file), but when using >> MASSIFFMODE the program ends with a segmentation fault, see below: >> >> > ./PTMProphetParser MASSDIFFMODE VERBOSE interact-01A.pep.xml interact. >> mod.pep.xml >> >> >> INFO: Applying PSM specific mass offset and tolerance ... >> INFO: Writing file interact.mod.pep.xml ... >> >> >> Creating 1 threads >> Wait for threads to finish ... >> INFO: Reading file interact-01A.pep.xml ... >> INFO: processed 31000/31545 spectrum_queries >> INFO: done ... >> INFO: Computing EM Models ... >> Iterating PTM Model: ....5....10....15....20....25....30....35....40.... >> 45....50....55....60....65....70....75....80....85....90....95....INFO: >> done ... >> INFO: done ... >> >> >> Creating 1 threads >> Wait for threads to finish ... >> INFO: Reading file interact-01A.pep.xml ... >> Segmentation fault (core dumped) >> >> Is there any other option that we should add to the run ? >> >> Thanks >> >> -- >> 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 spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
