[Bioperl-l] Root::IO tempfile error

[kaboroev at sfu.ca]

Hi all,
i have a script that uses both the Standalone blast and Lagan wrappers for
pairwise alignments.  However, every so often (varies when it will occur) i
receive an error that the temp file for one of the input sequences cannot be
found.	i have the error for the lagan below.  also if i get around the
throw (catch with an eval {}) and continue, the next instance of an
alignment does not necessarily fail.  Also, if the suggested remedy is
update my bioperl, when i install the second copy (from a non-root account)
how do i ensure that the the newer version of the modules are used (I'm
asking because i already tried and could not force my scripts to use those
modules located in my home directory)

keith
==============================
==============================
Use of uninitialized value in -e at /home/boroevich/perllib/Lagan.pm line
440 (#2)
    (W uninitialized) An undefined value was used as if it were already
    defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.

    To suppress this warning assign a defined value to your variables.

    To help you figure out what was undefined, perl tells you what operation

    you used the undefined value in.  Note, however, that perl optimizes
your
    program and the operation displayed in the warning may not necessarily
    appear literally in your program.  For example, "that $foo" is
    usually optimized into "that " . $foo, and the warning will refer to
    the concatenation (.) operator, even though there is no . in your
    program.

Uncaught exception from user code:

------------- EXCEPTION  -------------
MSG: Could not open /tmp/900CWxCW1G for reading: No such file or directory
STACK Bio::Root::IO::_initialize_io
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm:260
STACK Bio::AlignIO::_initialize
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:389
STACK Bio::AlignIO::new /usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:325
STACK Bio::AlignIO::new /usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:338
STACK Lagan::_runlagan /home/boroevich/perllib/Lagan.pm:410
STACK Lagan::_generic_lagan /home/boroevich/perllib/Lagan.pm:328
STACK Lagan::lagan /home/boroevich/perllib/Lagan.pm:207
STACK toplevel ./update_alignments:214

--------------------------------------
	Bio::Root::Root::throw('Bio::AlignIO::fasta=HASH(0x9f597fc)', 'Could
not open /tmp/900CWxCW1G for reading: No such file or dire...') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 260
	Bio::Root::IO::_initialize_io('Bio::AlignIO::fasta=HASH(0x9f597fc)',
'-file', '/tmp/900CWxCW1G', '-format', 'fasta') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm line 389
	Bio::AlignIO::_initialize('Bio::AlignIO::fasta=HASH(0x9f597fc)',
'-file', '/tmp/900CWxCW1G', '-format', 'fasta') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm line 325
	Bio::AlignIO::new('Bio::AlignIO::fasta', '-file', '/tmp/900CWxCW1G',
'-format', 'fasta') called at /usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm
line 338
	Bio::AlignIO::new('Bio::AlignIO', '-file', '/tmp/900CWxCW1G',
'-format', 'fasta') called at /home/boroevich/perllib/Lagan.pm line 410
	Lagan::_runlagan('Lagan=HASH(0x9f4bc08)', 'lagan.pl', ' -order "-gs
-7 -gc -2 -mt 2 -ms -1"  -recurse "(12,0,25,0),(13,...', '/tmp/FoEbuF3Gzc',
'/tmp/lIXp1wXIvh') called at /home/boroevich/perllib/Lagan.pm line 328
	Lagan::_generic_lagan('Lagan=HASH(0x9f4bc08)', 'lagan.pl',
'/tmp/FoEbuF3Gzc', '/tmp/lIXp1wXIvh') called at
/home/boroevich/perllib/Lagan.pm line 207
	Lagan::lagan('Lagan=HASH(0x9f4bc08)',
'Bio::PrimarySeq=HASH(0x9f5dc3c)', 'Bio::PrimarySeq=HASH(0x9f59acc)') called
at ./update_alignments line 214