Thank, Eric.
I tried updating pepXML file, also tried updating parameter files. Neither
brought me luck.
These are the outputs.
Shiliang
Output Files
-
*c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.tandem.pep.xml*
[ PepXML
<http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.tandem.pep.xml>
]
Command 1 [Thu Feb 25 22:48:21 2016] [ Show / Hide ]
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa&&
c:\Inetpub\tpp-bin\updatepaths.pl -d
c:/Inetpub/wwwroot/ISB/data/class/dbase/ipi.HUMAN.fasta -v -p
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/LD-CS-150324_Medimmune_P12_Expt8_F10_151206172438.tandem.pep.xml
*
*Command Successful*
RETURN CODE:0
All commands finished at *Thu Feb 25 22:48:21 2016*
Output for job id FK7DCY2HP_20160225-233101
Output Files
- *c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/tandem_params.xml*
[ Params
<http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=editparams&workdir=c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa&file=tandem_params.xml>
]
- *c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/taxonomy.xml* [
View <http://localhost/ISB/data/SLE/Expt8/QEHF/tpp_twa/taxonomy.xml> ]
Command 1 [Thu Feb 25 23:31:01 2016] [ Show / Hide ]
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa&&
c:\Inetpub\tpp-bin\updatepaths.pl -d
c:/Inetpub/wwwroot/ISB/data/class/dbase/ipi.HUMAN.fasta -v -p
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/tandem_params.xml *
*Command Successful*
RETURN CODE:0
Command 2 [Thu Feb 25 23:31:01 2016] [ Show / Hide ]
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa&&
c:\Inetpub\tpp-bin\updatepaths.pl -d
c:/Inetpub/wwwroot/ISB/data/class/dbase/ipi.HUMAN.fasta -v -p
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa
c:/Inetpub/wwwroot/ISB/data/SLE/Expt8/QEHF/tpp_twa/taxonomy.xml *
*Command Successful*
RETURN CODE:0
On Thursday, February 25, 2016 at 11:08:16 PM UTC-5, Eric Deutsch wrote:
>
> Can you post the output of the [Update Paths] job?
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>
> *From:* Shiliang Wang [mailto:[email protected] <javascript:>]
> *Sent:* Thursday, February 25, 2016 8:06 PM
> *To:* spctools-discuss <[email protected] <javascript:>>
> *Cc:* [email protected] <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:* [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
>
> · --
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