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I am trying to use bbmap (pileup.sh in= my.fa out=new.txt) to check the sequencing depth of assembly scaffolds derived from illumina reads.

Using Linux, I installed java jdk as you see:

$ java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

Also, I installed bbmap module.

When I tried to run the pipeline : pileup.sh in= my.fa out=new.txt, I got this error :

Error occurred during initialization of VM
Unable to allocate 207104KB bitmaps for parallel garbage collection for the requested 6627328KB heap.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

How can I fix this error?

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  • Please start with OS/release details (they provide a huge clue as to your software stack). This is not a generic GNU/Linux support site.
    – guiverc
    Jul 10, 2020 at 1:57

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