After Downloading via Docker (and singularity), Fatal Error Appears: No such file or directory

[bioinfo-fiend]

After downloading verifybamid2 both ways either via docker or singularity, I continue getting an error. I tried initially via source code but this does not work either as I come across htslibrary issue when trying to run the make command, as described in previous issue as seen here https://github.com/Griffan/VerifyBamID/issues/18

FATAL ERROR -
Failed opening file /hpc/annotation/variants/resources/gnomad_hg38_exome.r2.1.AF_0.01-0.2.biallelic.vcf.gz - No such file or directory

Exiting due to ERROR:
    Exception was thrown

Download via singularity:

singularity pull docker://griffan/verifybamid2

Command to run image

singularity exec verifybamid2_latest.sif VerifyBamID \
 --RefVCF /hpc/annotation/variants/resources/gnomad_hg38_exome.r2.1.AF_0.01-0.2.biallelic.vcf.gz \
 --Reference /hpc/references/hg38bundle/v0/Homo_sapiens_assembly38.fasta

[Griffan]

Does this cmdline work on your side?

docker run -v  /localPath/localDirectory:/VerifyBamID/localDirectory  griffan/verifybamid2:v1.0.6 VerifyBamID --SVDPrefix /VerifyBamID/resource/1000g.phase3.10k.b37.vcf.gz.dat --BamFile  /VerifyBamID/localDirectory/targetSample.bam --Reference  /VerifyBamID/localDirectory/hs37d5.fa 

[bioinfo-fiend]

I get the following error with singularity:

Digest: sha256:c208ca10a0351ea0c694b43d877fb8098b28c75482374cdd22172d524f48eecc
Status: Downloaded newer image for griffan/verifybamid2:v1.0.6
docker: Error response from daemon: Mounts denied:
The path /localPath/localDirectory is not shared from the host and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> Resources -> File Sharing.
See https://docs.docker.com/desktop/mac for more info.
ERRO[0009] error waiting for container: context canceled

[bioinfo-fiend]

Latest error with Singularity/Docker

Open file:/hpc/algorithms/VerifyBamID/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat.bed failed, exit

Command line:

singularity exec verifybamid2_latest.sif VerifyBamID \ 
--BamFile /hpc/resources/testWXS.bam \
--Reference /hpc/Homo_sapiens_assembly38.fasta \
--SVDPrefix /hpc/algorithms/VerifyBamID/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat

[bioinfo-fiend]

there was an issue with the mount where I was running on the hpc, will close this issue then.