Failed to pull singularity image

[gabriellovate]

I am having the following error when running What The Phage on Singularity with Slurm:

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name multifractal-metaphinder-0.1.img docker://multifractal/metaphinder:0.1 > /dev/null
  status : 255
  message:
    [34mINFO:    Starting build...
    time="2020-08-20T11:04:51-03:00" level=warning msg="\"/run/user/2324\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/2324: no such file or directory: Trying to pull image in the event that it is a public image."
    time="2020-08-20T11:04:53-03:00" level=warning msg="\"/run/user/2324\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/2324: no such file or directory: Trying to pull image in the event that it is a public image."
    Getting image source signatures
    Skipping fetch of repeat blob sha256:35c102085707f703de2d9eaad8752d6fe1b8f02b5d2149f1d8357c9cc7fb7d0a
    Skipping fetch of repeat blob sha256:251f5509d51d9e4119d4ffb70d4820f8e2d7dc72ad15df3ebd7cd755539e40fd
    Skipping fetch of repeat blob sha256:8e829fe70a46e3ac4334823560e98b257234c23629f19f05460e21a453091e6d
    Skipping fetch of repeat blob sha256:6001e1789921cf851f6fb2e5fe05be70f482fe9c2286f66892fe5a3bc404569c
    Skipping fetch of repeat blob sha256:f54761c28494735cc0f9c33ffe9936469de5a9d33ee8923a3575942bdba83fbc
    Skipping fetch of repeat blob sha256:1d553beff983d67de54f7aa9a9c0dcab926b1357e94e2fa2e2f8e0c6fb5195d8
    Copying config sha256:3a2ddae28471da3990c5c79b1b079741074a8b65c8123f8cbe9cf40d55abdc9b
    
     0 B / 3.24 KiB 
     3.24 KiB / 3.24 KiB  0s
    Writing manifest to image destination
    Storing signatures
    FATAL:   Unable to pull docker://multifractal/metaphinder:0.1: conveyor failed to get: no descriptor found for reference "acd152bf60aaf06e25091fb3281d16b2a59e5af68ebdb6d7b7cbbfaa36128f61"

I am not sure if the problem is in my end though.

[replikation]

• hi can you run WtP via --setup -profile slurm,singularity first to pre-download all images first and check if the bug persists?
• singularity has sometimes issues while building them - not sure why

[replikation]

• closing this, please reopen if error exists

[lfenske-93]

Hi, I have a similar problem.

Error executing process > 'setup_wf:vibrant_download_DB' 

Caused by: 
Failed to pull singularity image 
command: singularity pull  --name multifractal-vibrant-0.5.img.pulling.1707995221890 docker://multifractal/vibrant:0.5 > /dev/null
status : 255   
message:  
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly eq
ERROR: You must install squashfs-tools to build imagesuivalent images.
ABORT: Aborting with RETVAL=255
ERROR: pulling container failed! 

I checked everything and squashfs-tools seems to be installed.

When I try the setup command it runs into the same error. Do you have any idea what the problem might be?

Greetings,
Linda

[replikation]

@hoelzer are you able to run the setup on WtP with your singularity system?

[mult1fractal]

Hey,
what version of singularity are you running on your PC. same retval error

[lfenske-93]

Hi,

singularity version 3.7.0

So it seems to be a compatibility problem.

[hoelzer]

Hey, I just tried:

nextflow run replikation/What_the_Phage -r v1.2.3 --cachedir /biolibs/mf1/singularity/wtp -profile slurm,singularity --databases /scratch/hoelzerm/databases/wtp/nextflow-autodownload-databases --workdir work --setup

and it downloaded all the images just fine.

Completed at: 16-Feb-2024 15:48:52
Duration    : 1h 33m 40s
CPU hours   : 1.6
Succeeded   : 2

singularity --version
singularity-ce version 3.10.3-focal

[hoelzer]

But when I then execute the pipeline, I have another problem ;)

Error for command "exec": unknown flag: --shm-size

In the step

[b2/ea4ba1] process > input_validation_wf:seqkit (20) [666%] 20 of 3, failed: 20 ✘

Not sure why this is happening. I am otherwise running nf pipelines w/ singularity just fine on the same cluster.

[hoelzer]

In the .command.run I can find

nxf_launch() {
    set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_NXF_DEBUG=${NXF_DEBUG:=0} singularity exec -B /scratch/hoelzerm/projects/2024-02-06-ONT-Q20-performance-test-RIBAP-WtP --shm-size 2g /biolibs/mf1/singularity/wtp/nanozoo-seqkit-0.13.2--cd66104.img /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash /scratch/hoelzerm/projects/2024-02-06-ONT-Q20-performance-test-RIBAP-WtP/work/76/e87a6c0f2cea34c164d8b110467df9/.command.run nxf_trace"
}

and there is this --shm-size flag. Not sure where it is coming from.

[hoelzer]

I checked porcov .command.run scripts and they dont have this flag.

[hoelzer]

Ah!

withLabel: seqkit { container = 'nanozoo/seqkit:0.13.2--cd66104' ; containerOptions = '--shm-size 2g' }

Is this necessary? It fails Singularity... apparently... I think bc this is a Docker parameter!