Hi,

I'm using the option --keep 2 but I can not find in the output directory the file. I would like to keep the "alignments.bam" or something similar in sam/bam.

Will you validate the --vcf option?

Example:

unicycler -1 R1.fastq.gz -2 R2.fastq.gz -o output --mode normal --vcf --keep 2 --spades_tmp_dir ${tmp}

Best!