Mutect2 error

[yannic-chen]

Description of the bug

Hello,

I am running the "standard" pipeline with many variant callers, but suddenly got an error with Mutect2. The same command has worked previously for me for before. The command I ran is:
nextflow run nf-core/sarek -profile docker --input samplesheet.csv --outdir EMB95_01-009_sarek --igenomes_base ~/references/ --tools "deepvariant,mpileup,haplotypecaller,mutect2,freebayes,strelka" -resume

I have attached the nextflow log.

Command used and terminal output

nextflow run nf-core/sarek    -profile docker    --input samplesheet.csv    --outdir EMB95_01-009_sarek --igenomes_base ~/references/ --tools "deepvariant,mpileup,haplotypecaller,mutect2,freebayes,strelka" -resume

Relevant files

nextflow.log

System information

No response

[asp8200]

The error msg is "error waiting for container: unexpected EOF". It seems a lot of people ran into that problem with Docker. What version of Docker are you using?

I suggest that you come on over in the Sarek Slack channel and discuss this issue. Cheers

[yannic-chen]

This is my docker version

Client: Docker Engine - Community
Version: 27.2.0
API version: 1.43 (downgraded from 1.47)
Go version: go1.21.13
Git commit: 3ab4256
Built: Tue Aug 27 14:15:15 2024
OS/Arch: linux/amd64
Context: default

Server:
Engine:
Version: 24.0.5
API version: 1.43 (minimum version 1.12)
Go version: go1.20.14
Git commit: a61e2b4
Built: Tue Jun 25 22:38:06 2024
OS/Arch: linux/amd64
Experimental: false
containerd:
Version: v1.6.21
GitCommit: 3dce8eb055cbb6872793272b4f20ed16117344f8
runc:
Version: 1.1.12
GitCommit:
docker-init:
Version: 0.19.0
GitCommit: de40ad0

If it is a docker problem, then how was I able to run the same command previously to success?

[asp8200]

Hmmm ... good question.

Can you at least run the following commands on your system:

nextflow run nf-core/sarek -r 3.4.3 -profile test,tools_tumoronly,docker --tools mutect2 --outdir results

and

nextflow run nf-core/sarek -r 3.4.3 -profile test,tools_tumoronly,docker --tools mutect2 --no_intervals --outdir results

Those tests (here and here) have been run for v3.4.3, so they should also work on your system.

[yannic-chen]

Both of the commands were completed successfully.

[asp8200]

Let's ask @pontus - he is good with computers 😁

[pontus]

Could this be the OOM-killer activating for something unexpected? sudo dmesg -T should give a hint.

[yannic-chen]

here is the output of that command.

dmesg.txt

[pontus]

Ok, thanks, so it wasn't OOM (although there were some interesting apparmor notices that might cause issues, but probably not here).

But it still looks like some form of stability issue (with docker). I haven't seen any reports of this kind of issue.

I don't have the energy right now to parse the log well enough so I'm certain, but from a quick look it seems like there are multiple tasks running at the same time as the mutect, could you change that so that not so many run simultaneously? (Changing either maxForks or cpu or memory for that task, this is expected to help if it's some form of overload causing timeouts yielding errors, but not causing out of memory kills.)

Alternatively if that doesn't work, you might try replacing the snap docker installation with an installation of docker engine from docker.io, I don't know that it should really help but there are spurious reports of issues with the snap setup.

[yannic-chen]

I ran the command again with -resume and it now completed without any issues.