Hi Felipe, Yes I made progress. The bug is really a simple fix, but I have other code changes dealing with multithreaded changes to iProphet that will make it much faster, but these changes are currently interfering with the multi threaded aspect of PTMProphet that are causing bugs that I have to first fix so that's been the hangup so far. Alternatively I can just give you the updated PTMProphet code that you can compile against the current SVN code version.
Let me know if you'd rather wait another week or so for me to debug this. David On Tue, Apr 9, 2019, 1:07 PM Felipe da Veiga Leprevost < [email protected]> wrote: > Hi David; > > Any progress with the new version ? > > Thanks > > On Saturday, March 30, 2019 at 1:58:14 PM UTC-4, Felipe da Veiga Leprevost > wrote: >> >> We are currently working on both environments, I would appreciate if you >> could send both versions to us. >> >> >> On Friday, March 29, 2019 at 6:30:02 PM UTC-4, David Shteynberg wrote: >>> >>> 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 < >>> [email protected]> 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 < >>>> [email protected]> 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 [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.
