Closed ErnieHsieh closed 7 months ago
Hey @ErnieHsieh thanks for your interest in the pipeline!
Which command did you try to run it? Using Conda or Docker or Singularity?
My guess is that at least Docker/Singularity should work.
Hello @hoelzer,
I used the command as below:
./nextflow run EBI-Metagenomics/emg-viral-pipeline -r v2.0.0 --fasta "/home/ernie/Downloads/wms-unknown-vOTUs.fasta" --cores 8 --max_cores 8 --memory 16 --output wms_output -profile local,singularity
And then it shows some error messages:
ERROR ~ Error executing process > 'preprocess:rename (1)'
Caused by: Process
preprocess:rename (1)
terminated with an error exit status (255)Command executed:
if [[ wms-unknown-vOTUs.fasta =~ .gz$ ]]; then zcat wms-unknown-vOTUs.fasta > tmp.fasta else cp wms-unknown-vOTUs.fasta tmp.fasta fi rename_fasta.py -i tmp.fasta -m wms-unknown-vOTUs_map.tsv -o wms-unknown-vOTUs_renamed.fasta rename
Command exit status: 255
Command output: (empty)
Command error: FATAL: While checking container encryption: could not open image /home/ernie/singularity/quay.io-microbiome-informatics-virify-python3-1.2.img: the image's architecture (amd64) could not run on the host's (arm64)
Work dir: /home/ernie/work/01/52ac4a1e33531ede0d608517940e98
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line-- Check '.nextflow.log' file for details
Not quite sure if I need to re-install anything or it does not support the version of ubuntu Linux 22.04.1 (AArch64/ARM64)? My VM is installed and ran in M2 Pro Mac mini.
Many thanks for the assistance.
Hey,
hm. this is probably a problem related to the M2 architecture, which is not yet well supported by (bio)conda packages and many bioinformatics tools. I have similar problems with my M2 Macbook Air. See also the recent discussion here:
https://github.com/bioconda/bioconda-recipes/issues/23454#issuecomment-1766266069
Thus, the containers we provide with the pipeline probably dont match with the architecture. I am afraid, there is currently not much we can do (but correct me @mberacochea if there are ways).
Hi,
Sure, I also think so. I will try it in other environments. Hopefully this issue can be resolved soon.
Many thanks for your comments!
Hi folks,
I just see this ticket. Have you tried using the "--platform" flag for docker? Something like: https://github.com/nf-core/rnaseq/blob/master/nextflow.config#L192
Using that you should be able to run it directly on MacOS, not sure if that is going to work on the Linux VM.
Cheers
Hi,
I was wondering if this useful pipeline would be possible to run on ARM64-based Linux VM? When I ran a test with --help it could work; but when I ran it on my dataset it would fail. Seem like it can't support the new ARM64 version?
Thanks.