HI, Joe:
Thanks for your response.
No, There are no more output. I checked the folder, no file was
changed although the output showed command successful.
I am running TPP_Setup_4.8.0.
Shiliang
On Tuesday, March 1, 2016 at 12:05:13 PM UTC-5, [email protected]
wrote:
>
> 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]
> <javascript:>> 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
>>>> -
>>>>
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>
>
>
> --
> Joe Slagel
> Institute for Systems Biology
> [email protected] <javascript:>
>
>
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