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Depth of Coverage java memory issue
I am running DoC walker on a multi-sample (384) bam file (~ 100 Gb). Even after assigning 200Gb to java memory (Xmx204800m) I get the following error:
ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java # ERROR
The relevant log file is also attached.
Its not that the programme does not start at all but it fails somewhere in between while running the job which is even more frustrating as it wastes a lot of time rather than immediately prompting about this lack of enough memory.
Also the documentation for DoC mentions that it outputs 'summary: total, mean, median, quartiles, and threshold proportions, aggregated over all bases' but I only see mean coverage column in the partial output file. I want to know the median coverage but can't find any option to add this if it is not generated by default.