Hi Alex, Have you tried that latest version of TPP? If that one still fails then your processing could be exposing a potential new bug that we would certainly like to fix. Can you check that all your data files are there, non-empty, readable and complete. If there is a corrupted mzML/mzXML file and ASAPRatio cannot read a certain spectrum from the file this could also cause a bad crash. An easy way to troubleshoot this is to sort by file type and compare the sizes of the mzML/mzXML files, are they all about the same or are some much smaller. If it worked on this type of analysis before it should work again regardless of the instrument you used to acquire your data.
Good luck, -David On Wed, Nov 21, 2012 at 8:44 AM, kshitiz tyagi <[email protected]> wrote: > just curiois! have u tried XPRESS?? On large datasets, in our lab, ASAP > gave us a lot of problems while XPRESS worked. > > > On Wed, Nov 21, 2012 at 4:41 PM, Alex <[email protected]> wrote: > >> Thanks Brain for your quick reply, >> >> I'm running a dimethylation experiment (Ligth+28, Heavy+32). Until now, I >> have been acquiring data with a QTRAP2000, and everything worked nicely >> using the static approach (but not much proteome coverage with this MS). We >> now got a VelosPRO Orbitrap, and I am reacquiring the same samples!!!. I'm >> running X!Tandem, and DB search worked so far for protein ID. When I >> ANALYZE peptides with ASAPratio, things crash after 2-3 hours with this >> message. Until now, I have always been using the STATIC approach (according >> to the many threads I have reviewed on this topic), where I repeat the DB >> search for the light and heavy using two different parameters search. It >> used to work fine with the QTRAP2000 data. Of course, my files with the >> orbitrap are much larger, so I was suspecting I was running into some >> memory issue (Im not sure what this Runtime is all about). >> >> I'll try with your approach, if you have any other ideas, welcome!!! >> >> Alex >> >> >> On Wednesday, 21 November 2012 10:40:06 UTC-4, Brian Hampton wrote: >> >>> I've never gotten the static option to work. I'm not sure how the >>> static option is intended to be used..... correctly e.g. What type of data >>> set. >>> >>> If you are doing two searches one with the static light and the second >>> with the static heavy isotope labels, you will have to redo the search and >>> do it as per the Tandem API where you set the light to be a static mod and >>> the mass difference between the heavy and light to be a variable mod. In >>> addition to giving results ASAPRatio can quantitate, it has been noted that >>> the second search method is more statistically sound because it increases >>> the size of the database as a result of the variable mods. >>> >>> Using the second search strategy has reduced ASAPRatio processing time >>> on my data sets from many hours to about a half hour. Also, using the >>> static option on Linux w/ TPP 4.5.2 ASAPRatio would complete after hours. >>> But I have problems with the viewers not working in Linux so after >>> switching to Win for the quan analysis, using TPP 4.6.1 the static option >>> always kicks out an error and quits. Feeding it search results as >>> mentioned above it all works and completes much more quickly. >>> >>> Why the static option doesn't work on our data sets is a mystery to me. >>> >>> Brian >>> >>> >>> On Nov 21, 2012, at 8:33 AM, Alex <[email protected]> wrote: >>> >>> I think my post didn't show up correctly. Here it goes again! >>> >>> Hi TTP community, >>> >>> I'm running some ASAPratio quant on a 2D-LC-MSMS experiment on windows >>> XP running TPP v4.5 RAPTURE rev 2, Build 201202031108 (MinGW). After a >>> couple of hours analysis I get the following error. Has somebody run >>> into this problem before??? Any ideas much appreciated!!! >>> >>> >>> Alex >>> >>> >>> Error Message: >>> >>> This application has requested the Runtime to terminate it in an unusual >>> way. >>> Please contact the application's support team for more information. >>> command "C:/Inetpub/tpp-bin/**ASAPRatioPeptideParser "interact.pep.xml" >>> -lKn -F -C -r0.1 -S -mK160.15137n33.06425" failed: No such process >>> command "C:/Inetpub/tpp-bin/**ASAPRatioPeptideParser "interact.pep.xml" >>> -lKn -F -C -r0.1 -S -mK160.15137n33.06425" exited with non-zero exit code: 3 >>> QUIT - the job is incomplete >>> command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -Op >>> -I1 -I4 -I5 -A-lKn-F-C-r0.1-S-mK160.**15137n33.06425 >>> 2DYeast01.tandem.pep.xml >>> 2DYeast02.tandem.pep.xml 2DYeast03.tandem.pep.xml >>> 2DYeast04.tandem.pep.xml 2DYeast05.tandem.pep.xml 2DYeast06.tandem.pep.xml >>> 2DYeast07.tandem.pep.xml 2DYeast08.tandem.pep.xml >>> 2DYeast09.tandem.pep.xml 2DYeast10.tandem.pep.xml 2DYeast11.tandem.pep.xml >>> 2DYeast12.tandem.pep.xml 2DYeast13.tandem.pep.xml >>> 2DYeast14.tandem.pep.xml 2DYeast15.tandem.pep.xml 2DYeast16.tandem.pep.xml >>> 2DYeast17.tandem.pep.xml 2DYeast18.tandem.pep.xml >>> 2DYeast19.tandem.pep.xml 2DYeast20.tandem.pep.xml 2DYeast21.tandem.pep.xml >>> 2DYeast22.tandem.pep.xml 2DYeast23.tandem.pep.xml >>> H2DYeast01.tandem.pep.xml H2DYeast02.tandem.pep.xml >>> H2DYeast03.tandem.pep.xml >>> H2DYeast04.tandem.pep.xml H2DYeast05.tandem.pep.xml >>> H2DYeast06.tandem.pep.xml H2DYeast07.tandem.pep.xml >>> H2DYeast08.tandem.pep.xml >>> H2DYeast09.tandem.pep.xml H2DYeast10.tandem.pep.xml >>> H2DYeast11.tandem.pep.xml H2DYeast12.tandem.pep.xml >>> H2DYeast13.tandem.pep.xml >>> H2DYeast14.tandem.pep.xml H2DYeast15.tandem.pep.xml >>> H2DYeast16.tandem.pep.xml H2DYeast17.tandem.pep.xml >>> H2DYeast18.tandem.pep.xml >>> H2DYeast19.tandem.pep.xml H2DYeast20.tandem.pep.xml >>> H2DYeast21.tandem.pep.xml H2DYeast22.tandem.pep.xml >>> H2DYeast23.tandem.pep.xml" failed: No >>> such process >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To view this discussion on the web visit https://groups.google.com/d/** >>> msg/spctools-discuss/-/**K9ou37m9EhEJ<https://groups.google.com/d/msg/spctools-discuss/-/K9ou37m9EhEJ> >>> . >>> To post to this group, send email to spctools...@googlegroups.**com. >>> To unsubscribe from this group, send email to spctools-discu...@** >>> googlegroups.com. >>> >>> For more options, visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>> . >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/1HV_Ukku1HAJ. >> >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > > > -- > Kshitiz Tyagi > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
