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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 '20 at 1:57
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There is not enough virtual memory space requested by an application thus the application fails to start. This usually happens during the application startup phase. Applications reserve a large amount of virtual memory for the JVM heap space during the startup phase.

Most of the time you can fix this problem by uninstalling the Java runtime and then reinstalling it all over again. You can also try increasing the amount of system memory allocated to the Java virtual machine by setting an environment variable.

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