SamStudio8
commented
2 years ago Hi @craigwindell, from your log it looks as though the latest containers for this version may not have been downloaded by Nextflow which might explain this error. I have downloaded the container we released for wf-human-variation-snp for v0.2.2 and cannot replicate your import error.
Can you check which containers have been downloaded to your Singularity cache dir? You can also try deleting any wf-human-variation images from your Singularity cache dir and starting the workflow again.
craigwindell
What happened?
snp:pileup_variants fails with python error: RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd ImportError: numpy.core._multiarray_umath failed to import ImportError: numpy.core.umath failed to import
nextflow launch script: cat < nextflow.config
process {
executor = "local"
}
executor {
\$local {
cpus = 48
memory = "128.G"
}
}
singularity {
runOptions = "-B ${TMPDIR}"
}
EOF
OUTPUT='results'
nextflow run epi2me-labs/wf-human-variation -r v0.2.2 \
-resume \
--threads 48 \
-profile singularity \
--snp --sv \
--phase_vcf \
--use_longphase \
--tr_bed demo_data/demo.bed \
--model demo_data/ont_r104_e81_sup_g5015 \
--bam demo_data/demo.bam \
--ref demo_data/demo.fasta \
--out_dir ${OUTPUT}
Environment: HPC with PBS Pro scheduler SUSE12 Singularity: singularity-ce version 3.10.2-1 Nextflow: 22.04.5
With v0.1.1 of the workflow, this error does not occur
Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
No response
Workflow Execution - Execution Profile
Singularity
Workflow Version
v0.2.2
Relevant log output