cihaterdogan
commented
3 months ago Please also find the log file here nextflow.log
Closed cihaterdogan closed 1 month ago
cihaterdogan
commented
3 months ago Please also find the log file here nextflow.log
vlshesketh
commented
3 months ago Hi @cihaterdogan, thank you for reporting this. It looks as if the reporting script is not dealing with the case when no CNVs are detected. I will update here when we have a fix for this.
vlshesketh
commented
1 month ago Hi @cihaterdogan, this has now been fixed in v2.0.0.
Operating System
Other Linux (please specify below)
Other Linux
Red Hat Enterprise 8.x
Workflow Version
v2.0.0
Workflow Execution
Other (please describe)
EPI2ME Version
No response
CLI command run
export NXF_SINGULARITY_CACHEDIR=Path/.singularity export SINGULARITY_TMPDIR=Path/.singularity export NXF_HOME=Path
OUTPUT=Su715_BTRC_215_AUD_F_results
./nextflow run epi2me-labs/wf-human-variation \ -w ${OUTPUT}/workspace \ -profile singularity \ --bam 'ONT_000_COGA_DNA150_Dec2023/Su715_BTRC_215_AUD_F_simplex_sup_5mc5hmc_m6A_unaligned.bam' \ --basecaller_cfg 'dna_r10.4.1_e8.2_400bps_sup@v4.3.0' \ --mod \ --ref 'hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna' \ --sample_name 'Su715_BTRC_215_AUD_F' \ --sv \ --snp \ --str \ --cnv \ --phased \ --sex female \ --threads 32 \ --bam_min_coverage 5 \ --out_dir ${OUTPUT}
Workflow Execution - CLI Execution Profile
singularity
What happened?
I was running the wf-human-variation pipeline as a job (with Slurm) on my institution's clusters with the following input
!/bin/bash
SBATCH --nodes=1
SBATCH --ntasks-per-node=1
SBATCH --cpus-per-task=32
SBATCH --time=0-24:00:00
SBATCH --mem=200gb
module load singularity/3.8.3 module load java/17.0.0
OUTPUT=Su715_BTRC_215_AUD_F_results
./nextflow run epi2me-labs/wf-human-variation \ -w ${OUTPUT}/workspace \ -profile singularity \ --bam 'ONT_000_COGA_DNA150_Dec2023/Su715_BTRC_215_AUD_F_simplex_sup_5mc5hmc_m6A_unaligned.bam' \ --basecaller_cfg 'dna_r10.4.1_e8.2_400bps_sup@v4.3.0' \ --mod \ --ref 'hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna' \ --sample_name 'Su715_BTRC_215_AUD_F' \ --sv \ --snp \ --str \ --cnv \ --phased \ --sex female \ --threads 32 \ --bam_min_coverage 5 \ --out_dir ${OUTPUT}
I successfully analyzed five samples using the same parameters with this tool but got the following error in one sample.
ERROR ~ Error executing process > 'cnv_spectre:makeReport (1)'
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?
yes
Other demo data information
No response