Hi Julia, The Sequest pipeline currently works with .out files only. What format is your sequest output in? We might have a Sqt2XML converter executable if you have sqt format.
-David On Wed, Dec 28, 2011 at 11:16 AM, [email protected] <[email protected]> wrote: > I want to use Sequest from TPP, thus I am using TPP in the same > computer where I have installed Proteome Discover (PD) 1.0 (with > Sequest). First, the output of sequest from PD is not *.out that is > necessary for conversion to pepxml. Does anyone know a way to convert > this file into pepxml? As I was unable to obtain this conversion, I > tryed to use Database search with SEQUEST in TPP. I got many errors, > such as " couldnt find sequest.exe at c;/xcalibur\systems\programs > \bioworksbrowser, although sequest is perfectely running at PD. Thus, > I created a folder at the above destination and copied the > sequest.exe. I also, created a sequest.params using a model at > http://proteomicsresource.washington.edu/sequest_release/release_201102.php. > (I just changed thedatabase destination folder ). Thus, I ran my mzxml > file and I got no results. Here is the message. I really appreciate if > someone could help me! > Best regards! And A happy new year! > > julia > > ------------ > > 2650 099% > 2651 100% > > Done. > > chmod g+w IT_20110824_06; cp c:/Inetpub/wwwroot/ISB/data/parameters/ > sequest.params IT_20110824_06 > cd IT_20110824_06; find . -maxdepth 1 -depth -name > "IT_20110824_06*.dta" -print | xargs --max-args=50 c:/xcalibur/system/ > programs/bioworksbrowser/sequest.exe -Pc:/Inetpub/wwwroot/ISB/data/ > parameters/sequest.params > > command "c:\Inetpub\wwwroot\..\tpp-bin\find.exe . -maxdepth 1 -depth - > name "IT_20110824_06*.dta" -print | xargs --max-args=50 c:/xcalibur/ > system/programs/bioworksbrowser/sequest.exe -Pc:/Inetpub/wwwroot/ISB/ > data/parameters/sequest.params" failed: Unknown error > command "cd IT_20110824_06; find . -maxdepth 1 -depth -name > "IT_20110824_06*.dta" -print | xargs --max-args=50 c:/xcalibur/system/ > programs/bioworksbrowser/sequest.exe -Pc:/Inetpub/wwwroot/ISB/data/ > parameters/sequest.params" failed with exit code 123 > Out2XML IT_20110824_06 1 > params file here: IT_20110824_06/sequest.params > > > Command Successful > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
