You can send me the source files you modified, I can compile the binaries here, that way I can save you some time.
On Tue, Apr 9, 2019, 6:19 PM David Shteynberg < [email protected]> wrote: > 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. > -- 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.
