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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!
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