Hi Eileen, Apparently after PeptideProphet analysis the dataset given doesn't contain any peptides with probability above 0.05 . See relevant message pasted below.
. . . 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 This could be for a number of reasons that one would need to look at the data to explore. The usual error is that there are few correct IDs in the search results. Some common points of failure are: incomplete or wrong database, too few spectra being searched, wrong search parameters (e.g. incorrect static mods). I hope this is helpful for resolving your error. -David On Tue, Sep 8, 2009 at 9:04 AM, Eileen Yue<y...@ohsu.edu> wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
