Hello Eileen, After you made the change to the sequest.params file you would need to reconvert your search results (out file directory) to pepXML for the pepXML files to reflect the parameter changes. Have you rerun Out2XML after the update to sequest.params?
Thanks, -David On Fri, Sep 4, 2009 at 11:52 AM, Eileen Yue<y...@ohsu.edu> wrote: > Thank you! > > I just tried to change the database into nonindexed in sequest.params and > keep all the results same. It does not work either though I have both > nonindexed and indexed database in the folder. > > > > > > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Brian Pratt > Sent: 04 September 2009 11:37 > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed > database > > > > That's right, the indexed database format is nonstandard and TPP doesn't > know how to read it. I think, though, that if you provide the nonindexed > version then you can probably have it both ways. > > On Fri, Sep 4, 2009 at 11:05 AM, Eileen Yue <y...@ohsu.edu> wrote: > > May I check with one question? > > I use bioworker to run the database search. I noticed that if I use the > indexed database search, after I load on the TPP to do the protein > probability analysis. TPP will not work. > > I can not use indexed database to run the search in order to load on TPP for > protein probability analysis,is this right? > > Thanks > Eileen > > -----Original Message----- > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Natalie Tasman > Sent: 04 September 2009 10:41 > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] Re: Failure with make > > > Hi Eliza, > > At this point, it might be worthwhile trying to compile the TPP on > another linux distribution that works well. For example, Ubuntu > 8.04. Then, I'd be sure to run the correct "install prerequisites" > file from tpp/installer_linux to make sure all the required system > packages are installed. > > Then again, it wouldn't hurt to run the correct "install > prerequisites" for your own system. Currently, the Ubuntu 9.04 script > seems to work for 9.10 also, if you're using that. > > > Good luck, > > Natalie > > > > On Sep 4, 2009, at 1:05 AM, Eliza wrote: > >> >> Mike - having an empty Makefile.config.incl didn't fix anything. I am >> still getting the error: make: *** No rule to make target `/ >> Makefile.pwiz.incl'. Stop. >> >> On Sep 1, 10:21 pm, Mike Coleman <tutu...@gmail.com> wrote: >>> Okay, this turned out to be useful. It appears that the contents of >>> your file 'Makefile.config.incl' is including itself (it appears to >>> be >>> a copy of 'Makefile.incl'). This recurses about 1000 times, at which >>> point you hit the file handle limit. The resulting error is >>> apparently ignored due to the '-include'. >>> >>> So, either make 'Makefile.config.incl' an empty file, or otherwise I >>> think it should be just a short file including a few variable >>> definitions. Also, verify that neither of these files is a symbolic >>> or hard link to the other. >>> >>> Probably this will fix things, or at least move things forward. >>> >>> Mike >>> >>> On Aug 31, 2:34 am, Eliza <blond...@googlemail.com> wrote: >>> >>>> OK I have added make.strace.gz to the file uploads. >>> >>>> On Aug 28, 6:34 pm, Mike Coleman <tutu...@gmail.com> wrote: >>> >>>>> Okay, if you really want to bring out the big guns, do something >>>>> like >>>>> this >>> >>>>> $ strace -f -s 1024 -v -o make.strace make >>> >>>>> and put the resulting 'make.strace' log somewhere where we can >>>>> look at >>>>> it. I think this is erroring out pretty quickly, so hopefully that >>>>> log won't be too huge. No promises, but this may very well clarify >>>>> what's going wrong. >>> >>>>> You'll have to install the strace package if it's not already >>>>> present. >>> >>>>> Mike >>> >>>>> On Aug 28, 4:59 am, Eliza <blond...@googlemail.com> wrote: >>> >>>>>> That doesn't make any difference. >>> >>>>>> On Aug 27, 8:12 pm, "Brian Pratt" <brian.pr...@insilicos.com> >>>>>> wrote: >>> >>>>>>> Yeah, that's what we use here too. Perhaps you could try it as >>>>>>> a different, >>>>>>> newly created user? It sounds like there is something peculiar >>>>>>> about your >>>>>>> shell setup. >>> >>>>>>> -----Original Message----- >>>>>>> From: spctools-discuss@googlegroups.com >>> >>>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza >>>>>>> Sent: Thursday, August 27, 2009 12:13 AM >>>>>>> To: spctools-discuss >>>>>>> Subject: [spctools-discuss] Re: Failure with make >>> >>>>>>> Bash >>> >>>>>>> On Aug 20, 11:55 pm, "Brian Pratt" <brian.pr...@insilicos.com> >>>>>>> wrote: >>>>>>>> We basically tried that already: Eliza says the suggested >>> >>>>>>>> export PWD=/opt/trans_proteomic_pipeline/src ; make all install >>> >>>>>>>> did not work. She also tried the "SRC_ROOT= $(shell pwd)" >>>>>>>> change to the >>>>>>>> makefile. There's something deeper going on. >>> >>>>>>>> Eliza, what shell do you use? I do see from googling that >>>>>>>> $PWD might be >>>>>>>> bash-specific, possibly there are other unintended bash >>>>>>>> dependencies. >>> >>>>>>>> Brian >>> >>>>>>>> -----Original Message----- >>>>>>>> From: spctools-discuss@googlegroups.com >>> >>>>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of Mike >>>>>>>> Coleman >>>>>>>> Sent: Thursday, August 20, 2009 1:26 PM >>>>>>>> To: spctools-discuss >>>>>>>> Subject: [spctools-discuss] Re: Failure with make >>> >>>>>>>> Eliza, >>> >>>>>>>> I'm still suspicious about the $PWD thing. If you're running >>>>>>>> 'make' >>>>>>>> normally, you might try something like >>> >>>>>>>> $ PWD=$(pwd) make ... >>> >>>>>>>> instead of just >>> >>>>>>>> $ make ... >>> >>>>>>>> to see whether that improves your situation. Alternatively, >>>>>>>> for the >>>>>>>> 'root' steps, you could do something like >>> >>>>>>>> $ sudo PWD=$(pwd) make ... >>> >>>>>>>> Mike >> >> > > > > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
