Qualimap out of memory

Question

[mar77]

I'm trying to use qualimap to do a quality check of my bam files generated with hisat2. I keep getting an 'out of memory' error message. I've seen that I can set desired memory size with the example being

qualimap --java-mem-size=1200M

Is anyone able to explain to me what the 1200m is in relation to? And what is the default for qualimap?

[Mensur Dlakic]

1200M is most likely 1200 Mb (or 1.2 Gb). Try setting it to 70-80% of your actual memory.

[from the mountains]

I don't usually use qualimap on rna data but 1.2 Gb is usually insufficient for my exome bams, regardless of the amount of available memory.