[Bioperl-l] Blast return codes

[Keith James]

>>>>> "Matthew" == Matthew Laird <lairdm at sfu.ca> writes:

    Matthew> Well, that's a step in the right direction, I have a
    Matthew> little more information now.  I added a $! before the $?
    Matthew> and received:

    Matthew> ------------- EXCEPTION ------------- MSG: blastall call
    Matthew> crashed: -1 No child processes /usr/local/blast/blastall
    Matthew> -p blastp -d
    Matthew> /usr/local/psort/conf/analysis/sclblast/sclblast -i
    Matthew> /tmp/8Dt6zF1U59 -e 1e-09 -o /tmp/ojP9n04LZh

    Matthew> STACK Bio::Tools::Run::StandAloneBlast::_runblast
    Matthew> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:640

    Matthew> This is where we get into Perl voodoo beyond my league,
    Matthew> "No child processes" - does that ring bells for anyone?
    Matthew> Thanks again.

That's interesting. I think we need to know your OS platform and Perl
version to get any further.

I think that the value left by a system call in $? is the same as if a
wait system call were made. No child processes is a Unix error code
(ECHILD) which can be caused by a wait, being reported by Perl.

What happens if you run the test for StandAloneBlast? (t/StandAloneBlast.t)

Keith

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -