Re: [spctools-discuss] PTMProphet 5.2.0. error
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 < david.shteynb...@systemsbiology.org> 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 < > leprevos...@gmail.com> 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 < david.s...@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 < > lepre...@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: 510152025303540. >> ...4550556065707580859095 >> 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...@googlegroups.com. >> To post to this group, send email to spctools...@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. >> > -- > 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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
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 < leprevos...@gmail.com> 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 < >>> david.s...@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 < lepre...@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: 510152025303540. > ...4550556065707580859095 > 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...@googlegroups.com. > To post to this group, send email to spctools...@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. > -- 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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
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 < >> david.s...@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 < >>> lepre...@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: 510152025303540. ...4550556065707580859095 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...@googlegroups.com. To post to this group, send email to spctools...@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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
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 < > david.s...@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 < >> lepre...@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: 510152025303540 >>> 4550556065707580859095INFO: >>> 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...@googlegroups.com . >>> To post to this group, send email to spctools...@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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
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: 510152025303540 >> 4550556065707580859095INFO: >> 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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
Hi David; Thanks for the quick reply. I would be glad to assist. How do you prefer to receive the file ? Maybe we could move the discussion to e-mail, I'm sure Alexey will be interesting to participate as well. On Tuesday, March 19, 2019 at 3:17:52 PM UTC-4, David Shteynberg 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 < > lepre...@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: 510152025303540 >> 4550556065707580859095INFO: >> 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-discu...@googlegroups.com . >> To post to this group, send email to spctools...@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.
Re: [spctools-discuss] PTMProphet 5.2.0. error
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: 510152025303540 > 4550556065707580859095INFO: > 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.
