When you used the extra verbose flag there should have been more output as to what the program was actually updating. Was there?
On Tue, Mar 1, 2016 at 8:11 AM, Shiliang Wang <[email protected]> wrote: > Hi, Joe: > > Thank you very much. > > I clicked the additional options selection box "Be extra > verbose about what is being done" following your suggestion when I tried to > update paths. It didn't work. > > Basically, this is what I did: > > 1. downloaded the zipped file from twa, and expanded all the > files in one folder, including: isb_default_input_kscore.xml, taxonomy.xml, > tandem_params.xml, .pepXML, .tandem.params, .tandem files; > > 2. copy the .mzML (I used this for tandem search in twa) file > to this same directory; > > 3. click [Files] [Update paths] tab, select the .pepXML (from > twa) for updating path; > > 4. select additional directories to search for, I input the > directory where all these files from twa sit; > > 5. specify new location of search database, I input the > location where the same protein database is saved that I used for database > search in twa; > > 6. for the additional option, I clicked the box "Be extra > verbose about what is being done"; > > 7. then, I clicked "update paths" button. > > The process ran. When I checked all the files in the folder, > nothing changed. If I open the .pepXML file, I was able to open it. > However, if I like to open the spectrum data of any peptide by clicking > "ION2", an error pops out as I showed in this thread. > > Did I do anything wrong? I also tried to select all the files > in the folder where all the expanded files sit in the 3rd step, it didn't > work either. > > Thank you very much. > > Shiliang > > > On Friday, February 26, 2016 at 6:52:52 PM UTC-5, > [email protected] wrote: >> >> When you run updatePaths, can you click on the additional options >> selection box "Be extra verbose about what is being done"? >> >> >> On Thursday, February 25, 2016 at 6:42:15 PM UTC-8, Shiliang Wang wrote: >>> >>> 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. > -- Joe Slagel Institute for Systems Biology [email protected] -- 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.
