Singularity fatal error

[amyhouseman]

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.3/docs/FAQ.md: Yes

Describe the issue: (A clear and concise description of what the issue is.) Running singularity on HPC returns this error, our HPC does not have docker so I assumed singularity would work:

Setup

• Operating system: Linux HPC
• DeepVariant version: 1.3.0
• Installation method (Docker, built from source, etc.): Singularity
• Type of data: WES

Steps to reproduce:

#!/bin/bash --login
#SBATCH -J AmyHouseman_deepvariant
#SBATCH -o %x.stdout.%J.%N
#SBATCH -e %x.stderr.%J.%N
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH -p c_compute_wgp
#SBATCH --account=scw1581
#SBATCH --mail-type=ALL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=HousemanA@cardiff.ac.uk     # Where to send mail
#SBATCH --array=1-33
#SBATCH --time=02:00:00
#SBATCH --time=072:00:00
#SBATCH --mem-per-cpu=32GB

module purge
module load singularity
module load parallel

set -eu

cd /scratch/c.c21087028/
BIN_VERSION="1.3.0"

singularity pull docker://google/deepvariant:"${BIN_VERSION}"

sed -n "${SLURM_ARRAY_TASK_ID}p" Polyposis_Exome_Analysis/fastp/All_fastp_input/List_of_33_exome_IDs | parallel -j 1 "singularity run singularity run -B /usr/lib/locale/:/usr/lib/locale/ \
  docker://google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \
--model_type=WES \
-ref=Polyposis_Exome_Analysis/bwa/index/HumanRefSeq/GRCh38_latest_genomic.fna \
--reads=Polyposis_Exome_Analysis/samtools/index/indexed_picardbamfiles/{}PE_markedduplicates.bam \
--output_vcf=Polyposis_Exome_Analysis/deepvariant/vcf/{}PE_output.vcf.gz \
--output_gvcf=Polyposis_Exome_Analysis/deepvariant/gvcf/{}PE_output.vcf.gz \
--intermediate_results_dir=Polyposis_Exome_Analysis/deepvariant/intermediateresults/{}PE_output_intermediate"

Error::

FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://google/deepvariant:1.3.0: pinging container registry registry-1.docker.io: Get "https://registry-1.docker.io/v2/": dial tcp 52.0.218.102:443: connect: network is unreachable

This may be an error on my behalf, but I have tried all other options and asked lots of different people.

Thanks, Amy

[amyhouseman]

My HPC team helped me with this error, just thought I'd add it here in case future people do this:

"The error message "connect: network is unreachable " is due to the compute nodes being closed to the internet (safety concerns). This means that you cannot download files while on the compute nodes. Our advice is to download any required input files first on the login nodes and then point to them in the job script."