Running on M1 macs

[f6v]

This is a long shot, but I'll try anyway. I'm trying to run this with Docker on M1 Mac. Here's the error:

➜  nextflow nextflow run nextflow-io/rnaseq-nf -with-docker
N E X T F L O W  ~  version 21.04.1
Launching `nextflow-io/rnaseq-nf` [tender_volhard] - revision: 1f5a9060aa [master]
 R N A S E Q - N F   P I P E L I N E
 ===================================
 transcriptome: /Users/f6v/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
 reads        : /Users/f6v/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/*_{1,2}.fq
 outdir       : results
 
executor >  local (3)
[78/8554c0] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [  0%] 0 of 1
executor >  local (3)
[-        ] process > RNASEQ:INDEX (ggal_1_48850000_49020000) -
[8b/e55b25] process > RNASEQ:FASTQC (FASTQC on ggal_liver)    [100%] 1 of 1, failed: 1
[-        ] process > RNASEQ:QUANT                            -
[-        ] process > MULTIQC                                 -
Error executing process > 'RNASEQ:FASTQC (FASTQC on ggal_gut)'

Caused by:
  Process `RNASEQ:FASTQC (FASTQC on ggal_gut)` terminated with an error exit status (139)

Command executed:

  fastqc.sh "ggal_gut" "ggal_gut_1.fq ggal_gut_2.fq"

Command exit status:
  139

Command output:
  (empty)

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
  /home/micromamba/.bashrc: line 50: PS1: unbound variable
  qemu: uncaught target signal 11 (Segmentation fault) - core dumped
  /Users/f6v/.nextflow/assets/nextflow-io/rnaseq-nf/bin/fastqc.sh: line 6:    59 Segmentation fault      fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}

Work dir:
  /Users/f6v/dev/nextflow/work/49/1b3cb66e3a0f16b96b37a01649e29b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

I'm new to Docker on ARM, but it seems like a wrong image is pulled? The base image should be available for arm64, should I force it somehow?

Thanks!

[pditommaso]

There's not an easy solution to this. Upstream problem is that Salmon is not available as natively compiled on ARM (via Bioconda). Therefore the container downloaded is the one for AMD/Intel arch which should run via qemu compatibility layer. Howeber the latter is failing due to a bug https://github.com/docker/for-mac/issues/5123

[pditommaso]

See also https://github.com/COMBINE-lab/salmon/issues/556

[f6v]

Thanks for getting back to me! Seems like I'm stuck with VPS instances for the time being.

[jorgeaguileraseqera]

it seems solved, see

https://nextflow.slack.com/archives/C02T98A23U7/p1652104483904449?thread_ts=1652102847.144039&cid=C02T98A23U7

[drpatelh]

I personally don't use a MAC but would this help? https://github.com/abiosoft/colima

You can set --arch options.

[pditommaso]

Best trick ever

export DOCKER_DEFAULT_PLATFORM=linux/amd64