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] <javascript:> [mailto: [email protected] <javascript:>] *On Behalf Of *Shiliang Wang *Sent:* Thursday, February 25, 2016 6:41 PM *To:* spctools-discuss <[email protected] <javascript:>> *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] <javascript:>. To post to this group, send email to [email protected] <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. 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.
