On Fri, May 27, 2011 at 3:27 AM, shashi shekhar <meshashi29@gmail.com> wrote:

if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem

How does the tool you are wrapping signal an error? Does it write to stderr and/or does it give a non-zero return code? The BLAST+ wrapper script looks for a non-zero return code, since BLAST+ will write harmless warnings to stderr which should not be treated as an error. Note the changes suggested on issue 325 have have not been made yet (in part because supporting PBS nicely would be hard). Peter