Exception in thread "main" java.lang.OutOfMemoryError: Java heap space (RAM 256GB, --window 25000, --maxTrain 500))

[Lei-Guo]

I got the "java.lang.OutOfMemoryError" no matter what settings I used or how much RAM I have. I installed HMMRATAC using "conda install -c bioconda hmmratac".

Below is my RAM and settings. RAM 256GB, --window 25000 (that is 1/100 of the default value), --maxTrain 500 (that is half of the default value)

Here is the error message: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

    at java.base/java.util.Arrays.copyOf(Arrays.java:3689)

    at java.base/java.util.ArrayList.grow(ArrayList.java:238)

    at java.base/java.util.ArrayList.grow(ArrayList.java:243)

    at java.base/java.util.ArrayList.add(ArrayList.java:486)

    at java.base/java.util.ArrayList.add(ArrayList.java:499)

    at FormatConverters.PileupToBedGraph.toMap(PileupToBedGraph.java:114)

    at FormatConverters.PileupToBedGraph.run(PileupToBedGraph.java:50)

    at FormatConverters.PileupToBedGraph.<init>(PileupToBedGraph.java:41)

    at WigMath.pileup.toBedGraph(pileup.java:217)

    at WigMath.pileup.build(pileup.java:206)

    at WigMath.pileup.<init>(pileup.java:71)

    at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:270)

[txizzy]

Hey, friend. I met this issues too. Please try to edit your conda config file at: ~/.conda/envs/envs_name/share/hmmratac-1.2.10-1/HMMRATAC. My launch parameters are: default_jvm_mem_opts = ['-Xms10g', '-Xmx200g'] You can follow my setting.