singularity fails to pull the hic-1.3.0 container

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

Start by reproducing the reported singularity pull --name nfcore-hic-1.3.0.img docker://nfcore/hic:1.3.0 command on the stated CentOS HPC environment. Review the provided pull output, the missing .nextflow.log, and the Singularity and Nextflow versions. Done means identifying the cause of the status 143 failure and recording a verified resolution or workaround.