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, jsl...@systemsbiology.org
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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