[Bioperl-l] blastall & StandAloneBlast
biolist at brinkman.mbb.sfu.ca
Wed Mar 2 13:36:43 EST 2005
I'm yet again being faced with a mysterious crash in blastall and Bioperl
that has been occuring for the past year. I'm receiving more reports from
people around the world using our software also experiencing this problem,
and the only answer I once received about the problem was, "That shouldn't
Anyhow, the error occurs when blastall is called from StandAloneBlast.pm,
Blast returns with a -1 error code which causes the Bioperl module to
throw an exception. We've had reports of this occurring on multiple Linux
distributions as well as on Solaris and OS X. But it doesn't happen on
all machine even if they're running the same distribution.
The crash output is below....
------------- EXCEPTION -------------
MSG: blastall call crashed: -1 /usr/local/blast/blastall -p blastp -d
/var/tmp/6m0QxSirC3 -e 1e-09 -o /var/tmp/AKCDNMCTyo -F F
STACK (eval) /usr/local/psort/bin/psort:320
STACK toplevel /usr/local/psort/bin/psort:320
The line in StandAloneBlast.pm we track the problem back to is:
$self->throw("$executable call crashed: $? $commandstring\n")unless
Odd thing is, Blast DOES run. If one comments out this line in
StandAloneBlast.pm, the execution succeeds perfectly fine. When I've
editted the error message being thrown to give more details, perl says the
error is related to a process not being able to be created, which is even
So, for some odd reason either blastall is passing back this -1 or perl is
giving it back to bioperl for whatever reason. The only advice we have
for people is to comment out this line in StandAloneBlast.pm.
Anyone have any thoughts of advice on where this problem is coming from?
SysAdmin/Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University
More information about the Bioperl-l