I am trying to run the package fastqcr in R. This provides a quality check output for fastq files that are input. I installed all of the suggested packages and followed the provided prompt from the package documentation. Below is my code and the error that I recieve:
fastqc(fq.dir = "~/ProteinEngineeringProject/PE_FASTQ_1",
qc.dir = "~/ProteinEngineeringProject/PE_FASTQ_QC")
Picked up JAVA_TOOL_OPTIONS: -Xss4196k -Xmx4196m -XX:+UseG1GC -XX:ParallelGCThreads=2 -XX:ConcGCThreads=2
ConcGCThreads (2) must be less than or equal to ParallelGCThreads (1)
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
I know that my paths are correct, and I do have Java installed on my local machine. I am running R from Posit workbench on a compluter cluster. Does anyone have any suggestions on how I can fix this?
I tried to ssh into my cluster from my terminal and execute the below option. No luck
JAVA_TOOL_OPTIONS=-XX:ConcGCThreads=1
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