We attempted to align some illumina reads with bwa using the multi-thread branch. We submitted the job to a cluster and it landed on a node with ~100 GB RAM and 48 cores. Ram usage exceeded the system resources and crashed the node.
We trimmed the data with dynamic trim but had not yet filtered out shortened reads, could this be responsible for the extreme RAM usage or is there a known issue with the mt branch?
(attempting to run this with the single thread sampe/samse took SO long that I suspect the memory issue might be present there as well.) I'm having a hard time diagnosing the cause of the problem.
We trimmed the data with dynamic trim but had not yet filtered out shortened reads, could this be responsible for the extreme RAM usage or is there a known issue with the mt branch?
(attempting to run this with the single thread sampe/samse took SO long that I suspect the memory issue might be present there as well.) I'm having a hard time diagnosing the cause of the problem.
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