Q: GC overhead limit exceeded

[Kayla-Morrell]

Use case
Background: I'm working on createing a workflow script (wdl) through AnVIL that will required the user to provide a reference genome along with a table locations of paired fastq samples (ideally stored on a Google bucket). Then the workflow script will run through all the necessary steps to run HMMRATAC (alignment with bwa, sorting, indexing, genomic information, and finally HMMRATAC). I've been working through the various steps but have run into some issues on the final step which is running HMMRATAC.

Data using: From the HMMRATAC paper I've saved the fastq pair samples SRR891269-SRR891274 to a google bucket. The reference genome I've used is from here which I've also saved to a google bucket.

Describe the problem
I was able to run through the workflow script using one of the sampler samples (SRR891274). The first issue I ran into was Java heap space so I adjusted the window parameter to 2500000, as described in the troubleshoot part of the HMMRATAC Guide. The script ran without any issue. Now that I'm trying to run the workflow over all the samples (including some of the larger ones likes SRR891269 and SRR891270) I've run into the Java heap space issue:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space 
        at WigMath.pileup.toBedGraph(pileup.java:214) 
        at WigMath.pileup.build(pileup.java:206) 
        at WigMath.pileup.(pileup.java:71) 
        at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:270)

as well as GC overhead limit exceeded:

Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at ATACFragments.FragPileupGen.scaleTracks(FragPileupGen.java:188)
	at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:375)

Describe the solution you tried
To try to debug I've been working with one larger sample (SRR891270). I solved the first issue Java heap space by setting the window to 250000, as shown here. But then this resulted in GC overhead limit exceeded. I tried increasing out memory allocation, shown here, going as high as 18GB with no success . I'm wondering if there are some default settings / memory requirements that are needed in order to be able to run HMMRATAC on such a large sample?

Please let me know if I can provide any additional information to help!