Hi Jimmy: Here I pasted the error for the search and you may have a look. Thank you for your help Eileen
...skipping 39 lines of output... -------------------------------------------------------------------------------- running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" command completed in 0 sec running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "C:\Xcalibur\database\combo_human_both.fasta.hdr"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 4 sec running: "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.0 JETSTREAM rev 2, Build 200807011544 (MinGW)) (xml input) (using degen pep info) . . . reading in c:/Inetpub/wwwroot/ISB/data/eileen/a549/EROLDSETTING/interact.pep.xml. . . . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+ spectra with min prob 0.05 no data - quitting command "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" failed: Operation not permitted command "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" exited with non-zero exit code: 1 QUIT - the job is incomplete Command FAILED -----Original Message----- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Jimmy Eng Sent: 04 September 2009 19:13 To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed database Eileen, It should work. As Brian suggested, post the error/log message so that we can see what the problem actually is to help you fix it. - Jimmy On Fri, Sep 4, 2009 at 1:15 PM, Eileen Yue<y...@ohsu.edu> wrote: > > Hi David: > Thank you for your suggestion! > > I just tried to rerun the pepxml after I changed the sequest. Params and then > continue with peptide analysis. I got the same problem with previous. > > Is there any other possible way to make this work? I am currently rerun the > database searching with only nonindexed database, but it is much much slower > than indexed database. > > Thank you for your help > > Eileen > > -----Original Message----- > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of David Shteynberg > Sent: 04 September 2009 12:34 > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed > database > > > 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 -~----------~----~----~----~------~----~------~--~---
