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Heap size #61

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sultandromeda opened this issue May 28, 2024 · 0 comments
Open

Heap size #61

sultandromeda opened this issue May 28, 2024 · 0 comments

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@sultandromeda
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Hi, I want assistance with the script that I run via the Shell command:

Script:
java -Xmx75G -jar ~/bin/DamageProfiler.jar -i ${1}.cram -o ./${1}.damage -r ./refseq.fa

Error:
Picked up JAVA_TOOL_OPTIONS: -Xmx2g
Welcome to DamageProfiler v1.1
Input file:RK5.PE.cram
Output folder:./RK5.PE.damage
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
at org.apache.commons.math3.util.ResizableDoubleArray.expand(ResizableDoubleArray.java:697)
at org.apache.commons.math3.util.ResizableDoubleArray.addElement(ResizableDoubleArray.java:442)
at org.apache.commons.math3.stat.descriptive.DescriptiveStatistics.addValue(DescriptiveStatistics.java:171)
at org.damageprofiler.io.OutputGenerator.computeSummaryMetrics(OutputGenerator.java:607)
at org.damageprofiler.calculations.StartCalculations.generateOutput(StartCalculations.java:374)
at org.damageprofiler.calculations.StartCalculations.startDamageProfilerOnSingleSpecies(StartCalculations.java:193)
at org.damageprofiler.calculations.StartCalculations.start(StartCalculations.java:149)
at StarterCLI.(StarterCLI.java:11)
at RunDamageProfiler.main(RunDamageProfiler.java:30)

   I want to understand why the tool always peaks up Xmx2g? 
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