[Bioperl-l] Blast return codes

[Matthew Laird]

Thanks for your assistance so far, I've been trying to find the difference 
between the machines that do work and the ones that don't.  The two most 
similar machines which some do and some don't work are a group of Red Hat 
9 machines.

The machines are running Red Hat 9 and Perl 5.8.0.  I've tried both 
bioperl 1.2.1 and 1.2.3.  The only other difference I could find was that 
perl was built from source on one of the machines that worked.  I tried 
doing that on one of the non-working machines and had no success.

I've tried running the StandAloneBlast.t, what environment variables do I 
need set?  I receive:
[root at ssb7121-5 t]# perl StandAloneBlast.t
1..10
ok 1
ok 2
ok 3
ok 4
Blast Database ecoli.nt not found at StandAloneBlast.t line 67.
Blast Database swissprot not found at StandAloneBlast.t line 72.
Blast databases(s) not found, skipping remaining  tests at 
StandAloneBlast.t line 76.
ok 5 # skip Blast or env variables not installed correctly
ok 6 # skip Blast or env variables not installed correctly
ok 7 # skip Blast or env variables not installed correctly
ok 8 # skip Blast or env variables not installed correctly
ok 9 # skip Blast or env variables not installed correctly
ok 10 # skip Blast or env variables not installed correctly

Obviously I need to set some variable so it can find the blast database.

Thanks again.

On 11 Dec 2003, Keith James wrote:

> >>>>> "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
> 
> 

-- 
Matthew Laird
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University