Please see the log:

I have successfully converted few but couple of samples generate the below 
error. Please let me know how to resolve this error and use the data? Is 
there anyting I can do by editing certain file / removing a particular file 
( if so how to find out which one is the culprit file)

# Commands for session 23QP7X0H5 on Fri Jul 19 16:31:54 2013
# BEGIN COMMAND BLOCK
###### BEGIN Command Execution ######
[Fri Jul 19 16:31:54 2013] EXECUTING: run_in 
c:/Inetpub/wwwroot/ISB/data/tutorial/tudca; c:\Inetpub\tpp-bin\Out2XML 
c:/Inetpub/wwwroot/ISB/data/tutorial/tudca/S6 1 -all -Etrypsin 
OUTPUT:
params file here: c:/Inetpub/wwwroot/ISB/data/tutorial/tudca/S6/sequest.params
Out2XML: unexpected file format, quitting

command "c:\Inetpub\tpp-bin\Out2XML 
c:/Inetpub/wwwroot/ISB/data/tutorial/tudca/S6 1 -all -Etrypsin" failed: 
Operation not permitted
END OUTPUT
RETURN CODE:256
###### End Command Execution ######
# All finished at Fri Jul 19 16:33:12 2013
# END COMMAND BLOCK


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