[Bioperl-l] StandAloneBlast.pm, bl2seq() and tempfiles on Win32/cygwin

Aaron J. Mackey amackey at pcbi.upenn.edu
Mon Feb 23 16:10:49 EST 2004

A colleague of mine is frustrated by attempting to use 
Bio::Tools::Run::StandAloneBlast to run bl2seq (Perl 5.8.2, bioperl 
1.4, windows XP, CygWin, etc.):

# synopsis:
$seq1 = $seqio->next_seq;
$seq2 = $seqio->next_seq;
$factory->bl2seq($seq1, $seq2);

StandAloneBlast successfully writes two temp files in /tmp, which have 
the sequence data and can be read by "less" or "cat" in another open 
window (with the main program suspended in debugger); however, if 
either the program code or I at the command line attempt to run bl2seq, 
it dies with "Cannot open file /tmp/7aasd78asd".  If I "cp" the temp 
files into new files, it runs fine.  Or, if I call 
$factory->bl2seq($file1, $file2) with filenames instead of seq objects, 
it also works fine.  I have tried various incarnations of closing the 
filehandles and Bio::SeqIO objects that StandAloneBlast.pm is using to 
generate these temp files, but to no avail (and of course, the 
tempfiles disappear upon program completion).

This is not the "failed to open tempfile; too many files open" error 
seen previously, and I also expect a fair number of "works for me" 
responses - please save your breath.

Thanks for any input,


More information about the Bioperl-l mailing list