singularity fails to pull the hic-1.3.0 container

[Kevin-Brockers]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/hic pipeline documentation

Description of the bug

I'm trying to run the pipeline v.1.3.0 on a hpc (centOS) using nextflow v20.07.1 and singularity v3.8.3-1.el7.
When I try to run the pipeline, it fails during pulling the singularity container

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

            NXF_OPTS='-Xms1g -Xmx4g' \

            nextflow -log {log} \
            run nf-core/hic \
            -r 1.3.0 \
            -c {input.config} \
            -profile singularity \
            --input '{params.file_dir}' \
            --split_fastq true \
            --genome 'mm10' \
            --digestion 'dpnii' \
            --chromosome_size {input.chromsizes} \
            --min_mapq 20 \
            --outdir {output.res_dir}

3. See error:

DEBUG nextflow.Session - Session aborted -- Cause: java.lang.IllegalStateException: Failed to pull singularity image
  command: singularity pull  --name nfcore-hic-1.3.0.img docker://nfcore/hic:1.3.0 > /dev/null
  status : 143

Expected behaviour

Pulling the singularity container and run the pipeline

Log files

Error executing process > 'getRestrictionFragments (genome.fa ^GATC)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name nfcore-hic-1.3.0.img docker://nfcore/hic:1.3.0 > /dev/null
  status : 143
  message:
    INFO:    Converting OCI blobs to SIF format
    INFO:    Starting build...
    Getting image source signatures
    Copying blob sha256:852e50cd189dfeb54d97680d9fa6bed21a6d7d18cfb56d6abfe2de9d7f173795
    Copying blob sha256:a6236801494d5ca9acfae6569427398c2942c031375b96cac887cafe1de5a09b
    Copying blob sha256:679c171d6942954a759f2d3a1dff911321940f23b0cdbe1d186f36bef0025124
    Copying blob sha256:5849476b4bf8a724cc5539bb32493e818e02460262ef5e14a17fb4eac19026ab
    Copying blob sha256:2ecb54bbaab44a001995fcd9d8e83da6dce4e03d2727b0bbcd848fca0cc46c2f
    Copying blob sha256:7882648efbd1a387aeafae96a636e8ebbd7582337059da2ba4302812240deef6
    Copying blob sha256:e986c92d97d6cbd17700165fbec181a8d06dbe4217326b5667a7ed6c902c0cd9
    Copying blob sha256:11eebdf879ec2bfb4045b52647b8a90f80374f524c469cf70e850030e15ca376
    Copying blob sha256:4a15ba5c0fe3d5f335cbc2396ff34a085cecca815534ad46c3ecb1f7b682eec7
    Copying blob sha256:78b5940813b5d40a77bcb718668a1befd9e83c174473bff62e8a2ecb1ee4e1ed
    Copying blob sha256:26f4c93356079736c43f429e785c51c958405353156892a51c8f33ed208e80df
    Copying blob sha256:ede563bd6c60745324b23ebffba3cc80a93ec8c5d5399af9e444f725bb5e1143
    Copying config sha256:ec2658cab61b58f9d73e2cbf4cc49f7a3eca9a23366dfff2882ed7b413779050
    Writing manifest to image destination
    Storing signatures
    2022/06/23 10:36:50  info unpack layer: sha256:852e50cd189dfeb54d97680d9fa6bed21a6d7d18cfb56d6abfe2de9d7f173795
    2022/06/23 10:36:51  warn xattr{etc/gshadow} ignoring ENOTSUP on setxattr "user.rootlesscontainers"
    2022/06/23 10:36:51  warn xattr{XXXXXX} destination filesystem does not support xattrs, further warnings will be suppressed
    2022/06/23 10:37:25  info unpack layer: sha256:a6236801494d5ca9acfae6569427398c2942c031375b96cac887cafe1de5a09b
    2022/06/23 10:37:25  warn xattr{etc/gshadow} ignoring ENOTSUP on setxattr "user.rootlesscontainers"
    2022/06/23 10:37:25  warn xattr{XXXXXX} destination filesystem does not support xattrs, further warnings will be suppressed
    2022/06/23 10:38:22  info unpack layer: sha256:679c171d6942954a759f2d3a1dff911321940f23b0cdbe1d186f36bef0025124
    2022/06/23 10:39:35  info unpack layer: sha256:5849476b4bf8a724cc5539bb32493e818e02460262ef5e14a17fb4eac19026ab
    2022/06/23 10:39:36  warn xattr{var/log/apt/term.log} ignoring ENOTSUP on setxattr "user.rootlesscontainers"
    2022/06/23 10:39:36  warn xattr{XXXXXXX} destination filesystem does not support xattrs, further warnings will be suppressed
    2022/06/23 10:39:36  info unpack layer: sha256:2ecb54bbaab44a001995fcd9d8e83da6dce4e03d2727b0bbcd848fca0cc46c2f
    2022/06/23 10:39:36  info unpack layer: sha256:7882648efbd1a387aeafae96a636e8ebbd7582337059da2ba4302812240deef6
    2022/06/23 10:39:36  info unpack layer: sha256:e986c92d97d6cbd17700165fbec181a8d06dbe4217326b5667a7ed6c902c0cd9
    2022/06/23 10:40:00  warn xattr{var/lib/apt/lists/auxfiles} ignoring ENOTSUP on setxattr "user.rootlesscontainers"
    2022/06/23 10:40:00  warn xattr{XXXXXXXX} destination filesystem does not support xattrs, further warnings will be suppressed
    2022/06/23 10:40:01  info unpack layer: sha256:11eebdf879ec2bfb4045b52647b8a90f80374f524c469cf70e850030e15ca376
    2022/06/23 10:40:01  info unpack layer: sha256:4a15ba5c0fe3d5f335cbc2396ff34a085cecca815534ad46c3ecb1f7b682eec7

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware: HPC
• Executor: slurm
• OS: CentOS Linux
• Version

Nextflow Installation

• Version: 20.07.1

Container engine

• Engine: Singularity
• version: v3.8.3-1.el7
• Image tag: nfcore/hic:1.3.0

Additional context

I also tried to pull the container independent of the nextflow pipeline and ran into the same error. Whereas