singularity fails to pull the hic-1.3.0 container
Kevin-Brockers opened this issue · comments
Kevin-Brockers commented
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I have checked the following places for your error:
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:
- 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}
- 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