BCFTools not running, but pipeline completing

[fmtwohig]

Description of the bug

There are some cases where the pipeline does not create a folder for BCFtools, but says the pipeline has completed. It does not generate a consensus. It will work for iVar. It seems like the snpeff build is not building the reference?

Command used and terminal output

echo Node list: $SLURM_JOB_NODELIST
echo Number of tasks: $SLURM_NTASKS

module load miniconda3
module load gcc/10.2.0-3kjq
module load singularity/3.7.0-bm53
conda init bash
conda activate viral_recon

which nextflow && nextflow -version

nextflow run nf-core/viralrecon -r 2.6.0 --input "/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/LCMV_ABQ_Sample_sheet_run2.csv" --outdir /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/ABQ/S --platform illumina --protocol metagenomic -profile singularity --skip_nextclade --fasta /xena/scratch/fmtwohig/LCMV_Stock_Seq_ABQ/LCMVABQS.fasta --kraken2_db /xena/scratch/fmtwohig/k2_pluspf_20240605.tar.gz --kraken2_db_name pluspf --skip_assembly --skip_blast --min_mapped_reads 10

Relevant files

.nextflow.log.zip

LCMV_ABQ_S (2).zip

LCMVABQS (2).zip

System information

HPC, slurm, singularity, 2.6, but also occurring on the new version