Singularity still calling docker

[fiddlinwill]

Hi, thank you for your time and work on this pipeline!

Our HPC cluster does not use docker and so I am using the --framework singularity option. However, it is not working on our system and I am getting the following error. Does the singularity option still require docker capability? Thank you!

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My command:

python /hpcdata/lpd_hi/Will/ssgenome/final_assembly_Strongy2.1_3k30xflye2.8/best_finder/Finder/run_finder --framework singularity --metadatafile Ss_best_metadata.csv --output_directory ss_best_finder_onlypennRNAseq --genome pilon124_round3_chromosomesnumbered.maskedsoft.fasta --genemark_path /sysapps/cluster/software/GeneMark-ES-suite/4.21 --genemark_license /sysapps/cluster/software/GeneMark-ES-suite/4.21/gm_key --cpu 16 --organism_model INV

Error:

Copying config a88d5db3ba done
Writing manifest to image destination
Storing signatures
2023/01/26 13:24:09 info unpack layer: sha256:ea362f368469f909a95f9a6e54ebe0121ce0a8e3c30583dd9c5fb35b14544dec
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack layer: unpack entry: bin: restore parent directory: restore xattr metadata: /hpcdata/scratch/searswj/tmp/build-temp-990069682/rootfs: unpriv.lsetxattr: invalid argument
INFO: Downloading library image to tmp cache: /hpcdata/scratch/searswj/tmp/sbuild-tmp-cache-249568772
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
2023/01/26 13:25:53 info unpack layer: sha256:ea362f368469f909a95f9a6e54ebe0121ce0a8e3c30583dd9c5fb35b14544dec
FATAL: Unable to handle docker://sagnikbanerjee15/finder:1.1.0 uri: while building SIF from layers: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack layer: unpack entry: bin: restore parent directory: restore xattr metadata: /hpcdata/scratch/searswj/tmp/build-temp-942281107/rootfs: unpriv.lsetxattr: invalid argument

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finder.err output

which: no docker in (/hpcdata/lpd_hi/Will/Apps/conda/bin:/hpcdata/lpd_hi/Will/Apps/conda/condabin:/cm/shared/apps/uge/8.6.15/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/sbin:/usr/sbin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:/hpcdata/lpd_hi/Will/Apps:/hpcdata/lpd_hi/Will/Apps:/hpcdata/lpd_hi/Will/Apps/Finder-finder_v1.1.0:/nethome/searswj/.local/bin:/nethome/searswj/bin)

[sagnikbanerjee15]

Hello @fiddlinwill,

All the docker images are hosted on Docker hub. Singularity will require access to the docker hub while downloading those images, which is why you see "docker" in the command.

Thank you.