Dear all, I have a problem with the memory management for a rule of a snakemake pipeline. Actually I have a C++ based tool to correct ChIP-seq and ATAC-seq signal for CNV in samples. I run it by the shell with the following rule:

# CNV correction
    rule M1_signal_correction_for_CNVs:
        input:
            dedup_BAM_shifted_sorted = ancient(...),
            dedup_BAM_shifted_sorted_index = ancient(...),
            tool_config_file = "path/to/the/configuration_file_of_the_tool.txt",
        output:
            regions = os.path.join(.../regions.bed),
            peaks = os.path.join(.../peaks.narrowPeak),
            CNV_profile = os.path.join(.../CNV_profile.txt),
            bedGraph = os.path.join(.../bedGraph.bdg)
        params:
            tool_path = config["tool_path"],
            basename = os.path.join(basename),
            sample = "{SAMPLES}"
        threads:
            config["tool_threads"]
        resources:
            mem_mb = 50
        shell:
            " {params.tool_path} {input.dedup_BAM_shifted_sorted} - {input.tool_config_file} {params.basename} --threads {threads} "

Everything is fine, except the fact that despite the meme_mb=50 parameter the RAM memory consuming in the server goes up to 190GB and then the server kills the process.

Consider also that I use the --resources mem_mb=50000 when I run the snakemake pipeline.

I tried to use also ulimit -v, but i does not work neither.

Does anyone have an idea of what I could do to limit the memory usage for this process?

Thank you in advance for your help