Too many file descriptors being opened?

[chinchliff]

Phlawd is failing with the following errors under 64 bit Mac OS X 10.7 and 10.8 (see error report below). There is some question of whether or not this may be due to phlawd failing to close some file descriptors as it runs, leading it to eventually hit the os-imposed limit on the number of open files, at which point it fails.

The problem does not seem to occur on Ubuntu Linux, so this os should not be used for testing solutions.

First step would be to go through the code, and make sure that every time a file is opened, it is also closed. If this doesn't solve the problem, then more testing will probably be necessary to diagnose the underlying cause.

---------------- user error report follows ------------------

I just encountered the same problem when using PHLAWD as Alexander Davila did (https://groups.google.com/forum/?fromgroups=#!topic/phlawd/oDjfYm9lmqw), and was curious if you'd been able to find a fix (in addition to the Ubuntu installation suggested by Cody)? Please let me know if you'd like me to add this to Alexander's post on the PHLAWD list.

I'm on a 64 bit Mac (OS 10.7.5) and have been using PHLAWD without problems for smaller datasets, but I just tried ramping it up assembling a larger/broader dataset and received the same output (more or less) as Alexander:

aligning
muscle -profile -maxmb 5000 -in1 mtSSUAsco_TEMPFILES/TEMP1.profile -in2 mtSSUAsco_TEMPFILES/TEMP2.profile -out mtSSUAsco_TEMPFILES/TEMPOUT.PROFILE 2> mtSSUAsco_TEMPFILES/muscle.out
6460 bytes
cleaning seqs for TEMPOUT.PROFILE
adding sequences to profile alignment table
aligning
muscle -profile -maxmb 5000 -in1 mtSSUAsco_TEMPFILES/TEMP1.profile -in2 mtSSUAsco_TEMPFILES/TEMP2.profile -out mtSSUAsco_TEMPFILES/TEMPOUT.PROFILE 2> mtSSUAsco_TEMPFILES/muscle.out
140735600420453 bytes
problem: empty file mtSSUAsco_TEMPFILES/TEMPOUT.PROFILE created

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and when I open the muscle.out file, I get (same as Alexander):

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

*** ERROR *** Cannot open 'mtSSUAsco_TEMPFILES/TEMP1.profile' errno=2

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And the TEMP1.profile file is also missing (like Alexander).