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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Nextflow docker: Error response from daemon #1532

Closed C2i-PeterChung closed 1 month ago

C2i-PeterChung commented 4 months ago

Description of the bug

hello I have an error when I ran the nextflow sarek pipeline:

`nextflow -bg run nf-core/sarek -r 3.4.0 -params-file params_samplesheet_F52_3.json -profile docker &

Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 125.

The full error message was:

Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (120236)'

Caused by: Process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (120236) terminated with an error exit status (125)

Command executed:

gatk --java-options "-Xmx3276M -XX:-UsePerfData" \ BaseRecalibrator \ --input 120236.converted.cram \ --output 120236_chr1_122026460-124977944.recal.table \ --reference Homo_sapiens_assembly38.fasta \ --intervals chr1_122026460-124977944.bed \ --known-sites dbsnp_146.hg38.vcf.gz --known-sites Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites Homo_sapiens_assembly38.known_indels.vcf.gz \ --tmp-dir . \

cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.(GATK) v//; s/ .$//') END_VERSIONS

Command exit status: 125

Command output: (empty)

Command error: docker: Error response from daemon: failed to create endpoint nxf-02MAUnCuusW7YHwLnsBbzWSA on network bridge: failed to add the host (vethe58dde8) <=> sandbox (veth83d3dac) pair interfaces: cannot allocate memory. time="2024-05-21T11:53:49+08:00" level=error msg="error waiting for container: context canceled"

Work dir: /data/hhgphk/runF52/work/00/8748af7adb7ffb4cbacc79d0fedbca

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh``

I tried to add the memory limit to docker file:

sudo nano /etc/default/docker
DOCKER_OPTS="--default-memory-limit=32768m --default-memory-swap=65536m"

My docker and nextflow version:

But it still does not work. I am new to nextflow, can anyone give me advice. Thanks.

Command used and terminal output

No response

Relevant files

No response

System information

Docker version 20.10.24, build 297e128

N E X T F L O W version 23.10.0 build 5889 created 15-10-2023 15:07 UTC (23:07 HKST) cite doi:10.1038/nbt.3820 http://nextflow.io

asp8200 commented 4 months ago

Hi @C2i-PeterChung. I would suggest that you come on over on Slack and discuss this problem with us.

Did you manage to get the profiles test and test_full running on your setup?

The memory-requirements for the process GATK4_BASERECALIBRATOR can be set in a config, but as a first step you might just try adding the option --max_memory '123.GB' to your nf-command. (Obviously, just replace 123 with whatever memory you have available.)

FriederikeHanssen commented 2 months ago

Is this still an issue?

FriederikeHanssen commented 2 months ago

This looks like it is a similar issue reported in #1519 . I will close this one and it can be tracked further in the other issue