Eileen, Can you paste the output including the 39 skipped lines?
The fact that one of the tools, RefreshParser, is looking to open "combo_human_both.fasta.hdr" indicates that changing the database back to the non-indexed version wasn't successful for whatever reason. 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 -~----------~----~----~----~------~----~------~--~---
