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Allocating memory for samtools sort in nextflow?

I have a nextflow pipeline which keeps failing due to memory issues at the FILTER step.

In some cases the input bam is extremely large (30G).

Question 1: Would it help to split the FILTER process into two FILTER1 and FILTER2 process each running just one samtools sort? I tried this with a test...and it didn't seem to make a difference for some reason.

Question 2: Is there something I can do limit samtools sort (paramters -m or -@) so that it does not go over the memory limit but also doesn't run too slowly?

 process FILTER {

        ...

        time '6h'
        cpus 8
        penv 'smp' 
        memory '32 GB'

        script:
        """
        #!/usr/bin/env bash
        samtools sort -n -m 5G -@ 12 "file1.bam" -o "$file1_sorted.bam"
        samtools sort -n -m 5G -@ 12 "file2.bam" -o "$file2_sorted.bam"
    """
samtools nextflow
• 2,678 views • link
written by Eliveri • Eliveri

2 answers

The -m value is per thread so samtools uses 5*12GB of RAM and that is more that the memory declaration of the process. Is is (imo) also unnecessarily many threads and RAM. Sort is reasonably fast and efficient with, say 4-8 cores and 1-2GB each.

• 0 views • link
written by ATpoint ATpoint

Thank you for breaking it down for me. I really learned a lot. I was indeed making the mistake of using more memory than declared.

• 0 views • link
written by Eliveri • Eliveri

Would it help to split the FILTER

it helps as you can parallelize the two sort . Or if the second one fails, the first one is still here.

there something I can do limit samtools sort (paramters -m or -@)

you should use what was declared in the process (cpu/memory).

    cpus 8
    memory '32 GB'
    afterScript "rm -rf TMP"
    script:
    """
    mkdir TMP
    samtools sort -n -m "${task.memory.giga}G" -@ "${task.cpus}" -T TMP/tmp "${input}" -o "TMP/out.bam"
    mv TMP/out.bam sorted.bam
    """
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. Making sure I do not use more memory than declared resolved the issue.

• 0 views • link
written by Eliveri • Eliveri

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