I struggling with the first step of running the test setup: nextflow run nf-core/proteinfamilies -profile test,docker --outdir protfam_test. I'm getting an 132 error which I think is an arm/amd64 issue. I have added runOptions = "--platform=linux/amd64" to my confing file but no luck. Any recommendations?

probably worth searching slack for “linux/arm64/v8” - looks like this has come up a few times?

I've no idea, I would also search for this in slack history as Ian suggested. It's a good thing you also asked this on the help channel..let's wait for further directions.

For info, this issue is repeatable for me too (presume we are using similar M3 laptops): Running:

nextflow run nf-core/proteinfamilies -profile test,docker --outdir protfam_test

Error:

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
  .command.sh: line 12:    35 Illegal instruction     mmseqs createdb mgnifams_input_small.fa mgnifams_test/mgnifams_test

Container:
  <http://quay.io/biocontainers/mmseqs2:17.b804f--hd6d6fdc_1|quay.io/biocontainers/mmseqs2:17.b804f--hd6d6fdc_1>

My comment above should be enough I think

Looks like this is already there under the

arm

profile.

docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }

I tried adding the

arm

profile to the command:

nextflow run nf-core/proteinfamilies -profile test,docker,arm --outdir protfam_test

I don’t get the warning about docker platform not matching, but I do still get the same error.

Hey Ian, do you have Rosetta enabled? In the docker client you need to enable the emulation of amd64.

Thanks for checking - but yes, already switched on:

there is another thing that we previously did with @Martin Beracochea:

export DOCKER_DEFAULT_PLATFORM=linux/amd64

it should be the same as

--platform=linux/amd64

AFAIK

Thanks, tried setting

DOCKER_DEFAULT_PLATFORM

- same error. Also just tried rebooting (you never know 😛)

Yep, I also tried the export DOCKER_DEFAULT_PLATFORM=linux/amd64. No improvement. 🤫

Ha - I’ve just got this to work by turning Rosetta OFF

Done via docker dashboard or using a command?

docker dashboard

Let me try.........

image.png

Love the ordering

image.png

Just done the same - running atm.

Awesome...weird, but awesome!

Completed successfully! Now where was I...?🤪