Recently I have used BWA and Bowtie2 to align simulated DNA sequencing data to test our sequencing simulator. I got some errors from both aligners:
submit.sh: line 48: 6881 Segmentation fault (core dumped)
terminate called after throwing an instance of 'std::bad_alloc'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134 or
(ERR): bowtie2-align died with signal 6 (ABRT)
I searched online and found most posts said this kind of error is related to the memory shortage, so I monitor the memory usage during the alignment. I found BWA consistently took ~9GB and BOWTIE2 consistently took ~5GB in total. I also ran a script to check the memory every 30 seconds and found both of the aligners occupied no more than 10% of the memory and there is always ~100GB memory available. I then tried using fewer threads (5 threads for example) and assign each thread 9GB memory but still got the same error. So I feel it is unlikely the memory issue.
The data I am aligning that throws out such error is having 100x coverage for human genome so a single fasts file would be 300-400GB. I also tried lower depth (e.g.15x coverage) data using the same simulator and the alignment can be done without issue. I am not sure if this is due to the simulated data is too deep but I feel it is just the number of total read and the aligner would take a longer time to finish rather than throw out an error.
Does anyone encounter a similar issue or know what might be an issue or can give some hint on how to fix it? Many thanks!