Error occurred during initialization of VM in "rule prepare_caller:"

[jennymoon90]

Hi,
Thank you for creating the varCA tool. I am trying to run it on my bulk ATAC-seq data. While I'm running the example data, I encountered error. Here is what I put in the command line, and what I see in the qlog file:

Command:
./run.bash --sge-cluster &

qlog: (Error part)
rule prepare_caller:
input: data/jurkat.chr1.bam, out/peaks/jurkat_chr1/peaks.bed, data/hg38.chr1.fa, callers/gatk
output: out/callers/jurkat_chr1/gatk
jobid: 0
wildcards: sample=jurkat_chr1, caller=gatk

^@^@^@^@^@^@^@^@^@activating conda environment: /u/project/ATAC/tools/varCA/.snakemake/conda/8d268094
Using GATInitializing parameters...
Loading reference genome ...
akemake/conda/8d268094/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/u/project/ATAC/tools/varCA/out/callers/jurkat_chr1/illumina/runWorkflow.py
e/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar HaplotypeCaller -L out/peaks/jurkat_chr1/peaks.bed -R data/hg38.chr1.fa -I data/jurkat.chr1.bam -O out/callers/jurkat_chr1/gatk/gatk.g.vcf.gz -ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation
Error occurred during initialization of VM
Could not reserve enough space for 4194304KB object heap
Using GATK jar /u/project/ATAC/tools/varCA/.snakemake/conda/8d268094/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /u/project/ATAC/tools/varCA/.snakemake/conda/8d268094/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar GenotypeGVCFs --include-non-variant-sites -L out/peaks/jurkat_chr1/peaks.bed -R data/hg38.chr1.fa -V out/callers/jurkat_chr1/gatk/gatk.g.vcf.gz -O out/callers/jurkat_chr1/gatk/gatk.vcf.gz
Error occurred during initialization of VM
Could not reserve enough space for 4194304KB object heap
Use of uninitialized value $sample_nowhitespace in substitution (s///) at /u/project/ATAC/tools/varCA/.snakemake/conda/8d268094/bin/var2vcf_valid.pl line 42.
Use of uninitialized value $sample in join or string at /u/project/ATAC/tools/varCA/.snakemake/conda/8d268094/bin/var2vcf_valid.pl line 112.
chr1.fa out/callers/jurkat_chr1/gatk jurkat_chr1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job prepare_caller since they might be corrupted:
out/callers/jurkat_chr1/gatk
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

The errors seem to be memory issue with JAVA. I'm not very familiar with python/snakemake, and I couldn't figure out where to set the memory parameter in the pipeline. Could you help with that? Also how big of a node shall I request to run through the example data? Currently I have requested 40GB.

Thanks a lot,
Jenny