[Bioperl-l] Blast return codes

[Joseph Bedell]

Hi Matthew,

I didn't see that anyone answered this question for you. See my comments
below.

>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>bounces at portal.open-bio.org] On Behalf Of Matthew Laird
>Sent: Friday, December 05, 2003 2:27 PM
>To: bioperl-l at bioperl.org
>Subject: [Bioperl-l] Blast return codes
>
>This is on the fringe of being off-topic... but still relivant. :)
>
>I've been trying to google around to find documentation regarding
return
>codes Blast gives upon exit.  Is there a list of return codes and
>conditions that cause non-zero return codes?

No, there is no such list. We recently wrote an O'Reilly book on BLAST
but we did not track down the return codes. We'll probably do that for
the next edition. ;)

>
>The reason I ask is I'm having a problem calling Blast from bioperl.
For
>some reason Blastall is returning a -1 exit code which of course causes
>bioperl to throw an exception.  However I have modified my local
install
>of bioperl to tell me the exact command that was being run.  I've then
run
>this exact command with the exact same input files from the command
line
>and a standard 0 exit code is returned.  Might anyone have any thoughts
on
>why Blastall would be returning a -1 exit code?

I believe that all the return codes from blastall are positive integers.
A -1 return code may signify a problem with the system call from PERL.
The error messages are usually pretty comprehensive. Can you send the
error message that's produced?

Thanks,
Joey

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Joseph A Bedell, Ph.D.
Director, Bioinformatics
Orion Genomics, LLC
4041 Forest Park Ave.
St. Louis, MO 63108
(314)615-6979; fax:(314)615-6975
http://www.oriongenomics.com
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~