Open samuelecancellieri opened 3 weeks ago
@samuelecancellieri It looks as though the Nextflow process is unable to write to your assigned TMPDIR.
mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/bcftools.FFZZJf) failed: No such file or directory
You should be able to either:
--bind <YOUR TMPDIR>
to the containerOptions directive (https://www.nextflow.io/docs/latest/process.html#containeroptions)
Operating System
Other Linux (please specify below)
Other Linux
Red Hat Enterprise Linux 9.4
Workflow Version
2.2.3
Workflow Execution
Command line (Local)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-human-variation --bam /storage/sahuarea/samuele_cancellieri/fei_ffpes/nanopore_dna-seq/LYM1/20240510_1453_P2S-00885-A_PAS09250_ca256177/bam_pass/ --out_dir lym1_all_variant_calling --depth_intervals --sv --snp --cnv --sample_name lym1_pass --ref /storage/sahuarea/samuele_cancellieri/reference_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --bam_min_coverage 0 -resume -profile singularity
Workflow Execution - CLI Execution Profile
singularity
What happened?
the pipeline stops and report an error at "concat_refined_snp" step command.run.log
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
other (please describe below)
Other demo data information