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Old 06-08-2017, 12:15 PM   #1
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Location: fdsa

Join Date: Aug 2009
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Default Bio::DB::Sam crashes

Hello, List,

I have "inherited" a perl script that makes use of Bio:B::Sam. Under certain (as yet unknown) conditions, this script crashes (seg faults) during a call to $sam->get_features_by_location(...) (where my $sam=Bio:B::Sam->new(...)).

I can provide further details as needed, but my question is, has anyone else had a crash similar to this and if so, can you tell me under what circumstances the crash occurred and what was done to rectify the situation?

In my situation, the program can crash when using the same input files and parameters, which leads me to suspect that the external factors play a role. The program is actually multi-threaded (forks, technically), and in practice some of the sub-processes run to completion while others experience the crash. Again, this makes me suspect that conditions external to the code are playing a role, e.g. memory or the number of open file descriptors or something similar. To that end, however, we have increased both the amount of RAM on the machine and the global resource limit configurations settings (number of open file descriptors, number of available sub-processes, and so on) to no avail).

To anyone who has seen this behavior, your experiences would be much appreciated.

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