Hi Browser,

Yup, removing Bio::SeqIO doesn't resolve the crashes but it dramatically speeds up execution. Further, the program runs quite a bit deeper before crashing. I also tried reducing the number of threads in the BioPerl-less program, and found that the fewer threads active at any one time, the deeper execution can go. So, with just 3 threads it completes, but with 5 it terminates about 80% of the way through the dataset. That seems to suggest that the threads are using a lot of memory: is there a way of assessing the memory footprint of an individual threads?

Also, you had previously mentioned that it might be useful to just create a pool of threads at the front, and to reuse them. I'd like to try that out, but I'm unsure how to do that, and didn't see anything in perldoc threads, but I could have missed it. My thought here is that perhaps threads are "leaking" some memory on my system, and reusing threads might help identify that.

Many thanks (again) for your help

In reply to Re^6: Memory Usage in Regex On Large Sequence by bernanke01
in thread Memory Usage in Regex On Large Sequence by bernanke01

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