Offline setup fails, cannot fetch Singularity images

[axiao19]

I am downloading MetScale for the first time and am running into issues with the download of the Singularity images when I run python download_offline_files.py --workflow all

Error message Downloading singularity image fastqc_0.11.7--pl5.22.0_2.sif FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2: not a valid image manifest or image index OS Error fastqc_0.11.7--pl5.22.0_2.sif [Errno 2] No such file or directory: 'fastqc_0.11.7--pl5.22.0_2.sif' -> '../container_images/fastqc_0.11.7--pl5.22.0_2.sif'

Additional context I get this error for all the biocontainers (Trimmomatic, MultiQC, Khmer, MegaHIT, etc), but the database files are downloading properly.

Could you offer some guidance on the correct versions of the containers that I will need? Thanks!

[kternus]

Hi @axiao19, could you try running this command and share the results?

singularity version

[axiao19]

Thanks for the quick response! Here's the output: singularity version 4.0.1-jammy

[kternus]

Great, thanks! Can you try this command next? That is an equivalent command for what the metscale scripts are doing to download the singularity images.

singularity pull docker://quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2

[axiao19]

Thanks! Here's the output:

singularity pull docker://quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2 FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2: not a valid image manifest or image index

[kternus]

@axiao19 Thanks for bringing this issue to our attention!

We were able to replicate the error with singularity version 4.0.1 on ubuntu20. It seems to be happening on all the quay.io containers, but earlier versions of singularity (3.4.2-1) don't appear to have this problem. If you're able to use an older version of singularity, that might be a quick fix. Otherwise, we will post here when we find out more!

[axiao19]

Thanks for the quick response! Unfortunately, I don't have an older version on the system, so I will look forward to the updated post. Really appreciate your help and support!

[axiao19]

Thanks for your help on this issue. On a side note, could you share how much disk space and computing power is required for MetScale? I'm not having much luck when searching through the Wiki but I could have missed something!