Snakemake checkpoint (exited with non-zero exit code)

问题

I need to make a checkpoint in Snakemake at the step where chromosomes are scattered to call copy number variants with GATK:

rule all:
    input:
        'aggregated/chr1'

# step that gives non-zero exit code error
checkpoint scattering:
    input:
        interval = 'gcfiltered_{chr}.interval_list'
    output:
        directory('scatter_{chr}')
    shell:
        'mkdir -p {output} && '
        'gatk --java-options "-Xmx8G" IntervalListTools '
        '--INPUT {input.interval} '
        '--SUBDIVISION_MODE INTERVAL_COUNT '
        '--SCATTER_CONTENT 600 '
        '--OUTPUT {output}'

def aggregate_scatter(wildcards):
    checkpoint_output = checkpoints.scattering.get(**wildcards).output[0]
    return expand('scatter_{chr}/{i}/scattered.interval_list',
            chr=wildcards.chr,
            i=glob_wildcards(os.path.join(checkoint_output, '{i}/scattered.interval_list')).i)

# dummy rule to check if scattered files will be aggregated:
rule aggregate:
    input:
        aggregate_scatter
    output:
        "aggregated/{chr}"
    shell:
        "cat {input} > {output}"

But the scattering rule fails. It gives an error (exited with non-zero exit code) and removes the output, although the output is produced correctly. I tried adding || true, it did not work.

However, when I run the command outside of snakemake, it runs fine with 0 exit status:

mkdir -p scatter_chr1 && gatk --java-options "-Xmx8G" IntervalListTools --INPUT gcfiltered_chr1.interval_list --SUBDIVISION_MODE INTERVAL_COUNT --SCATTER_CONTENT 600 --OUTPUT scatter_chr1
echo $?

I use Snakemake 5.5.4 and GATK 4.1.2.0. Input file example (gcfiltered_chr1.interval_list):

@HD VN:1.6
@SQ SN:chr1 LN:122678785    UR:file:canFam3.fa  M5:e4671b339daa96b7f11eb0b68fd999d8
chr1    100000  100999  +   .
chr1    101000  101999  +   .
chr1    102000  102999  +   .
chr1    103000  103999  +   .
chr1    104000  104999  +   .
chr1    105000  105999  +   .
chr1    106000  106999  +   .
chr1    107000  107999  +   .
chr1    108000  108999  +   .
chr1    109000  109999  +   .
chr1    110000  110999  +   .
chr1    111000  111999  +   .
chr1    112000  112999  +   .
chr1    113000  113999  +   .
chr1    114000  114999  +   .
chr1    115000  115999  +   .
chr1    116000  116999  +   .
chr1    117000  117999  +   .
chr1    118000  118999  +   .
chr1    119000  119999  +   .
chr1    120000  120999  +   .

来源：https://stackoverflow.com/questions/57432036/snakemake-checkpoint-exited-with-non-zero-exit-code

标签

python

snakemake