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 <[email protected]> wrote: > > Can you post the output of the [Update Paths] job? > > Thanks, > Eric > > > From: Shiliang Wang [mailto:[email protected]] > Sent: Thursday, February 25, 2016 8:06 PM > To: spctools-discuss <[email protected]> > Cc: [email protected] > 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: [email protected] [mailto:[email protected]] On > Behalf Of Shiliang Wang > Sent: Thursday, February 25, 2016 6:41 PM > To: spctools-discuss <[email protected]> > 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
