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EBI-Metagenomics / emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Apache License 2.0
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Error executing process > 'annotate:hmmscan_viphogs (1)' #125

Closed christinepalermo closed 2 months ago

christinepalermo commented 4 months ago

Virify fails to pull the hmmer singularity image:

ERROR ~ Error executing process > 'annotate:hmmscan_viphogs (1)'

Caused by: Failed to pull singularity image command: singularity pull --name quay.io-microbiome-informatics-hmmer-3.1b2.img.pulling.1715869876184 docker://quay.io/microbiome-informatics/hmmer:3.1b2 > /dev/null status : 255 message: INFO: Converting OCI blobs to SIF format FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: unable to create new build: while searching for mksquashfs : exec: "mksquashfs": executable file not found in $PATH

-- Check '.nextflow.log' file for details .nextflow.log

mberacochea commented 2 months ago

Hi @christinepalermo

Apologies for a very delayed response. It seems that your singularity installation, it's missing mksquashfs. If you are running on an HPC cluster, you should contact your support team about this. Otherwise, you should try to re-install singularity or "squashfs-tools" which is the dependency that seems to be missing.

Another approach would be to use docker, if you have that installed.

Cheers