Thank you very much, Luis. I put .mzML file and .pepXML file in same directory and specify "the additional directory" to this directory. No lucky. I am using the same TPP version as we used in the Feb. workshop.
Shiliang On Thursday, February 25, 2016 at 11:25:30 PM UTC-5, Luis wrote: > > Hello, > I think it may work if you select the directory where the mzML files are > located under "Specify Extra Directories". What version of TPP are you > using? > Glad you are trying out TPP on the cloud! > --Luis > > > On Feb 25, 2016, at 20:07, Eric Deutsch <edeu...@systemsbiology.org > <javascript:>> wrote: > > Can you post the output of the [Update Paths] job? > > > > Thanks, > > Eric > > > > > > *From:* Shiliang Wang [mailto:shil...@gmail.com <javascript:>] > *Sent:* Thursday, February 25, 2016 8:06 PM > *To:* spctools-discuss <spctools...@googlegroups.com <javascript:>> > *Cc:* edeu...@systemsbiology.org <javascript:> > *Subject:* Re: [spctools-discuss] problem to open .pepXML file generated > by TPP twa with xml viewer > > > > Thank you very much, Eric. > > > > I did try to put the .pepXML and .mzML files in same directory and then > updated paths in Petunia. I also put tandem.params.xml, taxonomy.,xml, and > LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.tandem.param > in the same directory and updated path. I got same error message. > > > > It seems I didn't do the updating in correct way, however, the only option > is to "*Specify new location of search database*" in update_path window. > > > > I tried different files generated by TPP twa. I got same error message. > > > > > > Shiliang > > > On Thursday, February 25, 2016 at 10:33:22 PM UTC-5, Eric Deutsch wrote: > > Hi Shiliang, where are your mzML files on your local machine? > > > > I think that Petunia [Files] [Update Paths] is the right thing to do, but > you need to have the mzML files in that same directory to work I think. > > > > So, in the same directory as you have: > > LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.pep.xml > > (or perhaps the interact.pep.xml file) > > Also have: > > LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.mzML > > > > And then run Petunia [Files] [Update Paths]. Did you try that? > > > > Or where are you mzML files located? > > > > If that’s what you had, maybe someone who understands [Update Paths] > better can help. > > > > Regards, > > Eric > > > > > > > > > > *From:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] > *On Behalf Of *Shiliang Wang > *Sent:* Thursday, February 25, 2016 6:41 PM > *To:* spctools-discuss <spctools...@googlegroups.com> > *Subject:* [spctools-discuss] problem to open .pepXML file generated by > TPP twa with xml viewer > > > > HI, > > > > I ran database search on TPP twa, and got the .pepXML file, I > was able to open the .pepXML file and also able to open the spectrum data > by clicking the IONS2 of a peptide, Every thing worked well. After I > downloaded the .pepXML and other files to a local directory, I was able to > open .pepXML file. However, when I tried to open the spectrum data by > clicking the IONS2 of a peptide, I got the following error message. > > > > I was suggested to update paths in .pepXML using Petunia [Files] > [Update Paths]. The only option is to update database path. I updated it. > When I tried to open spectrum data in .pepXML table, I got the same error > message. > > > > Anyone can give me detail instruction? Which file need to be > updated for paths? the .pepXML file or the parameter file? Do I need to put > the .pepXML file in a particular folder or not? > > > > Thank you very much. > > > > Shiliang > > > > command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf > /mnt/tppdata/SLE/LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.tgz > "*LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.00469.00469.2.dta" > > /dev/null" failed: Operation not permitted > > > > > > Messages > > · Error - cannot read spectrum; tried direct .dta, from > mzML/mzXML/mzData and from .tgz > > · Verify that file path is correct. > > · *LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.00469.00469.2.dta > > · -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discu...@googlegroups.com. > To post to this group, send email to spctools...@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discu...@googlegroups.com <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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