I couldn’t get my polish.fasta while running merfin:

Here's the bash script I'm using to process:

#!/bin/sh
THREADS=60
MERGE_VCF_OUTPUT="/slurm/users/merfin/callsMat.vcf"
INPUT="/slurm/users/medaka/medaka.Mat/consensus.fasta"
READMER_DB="/slurm/users/NGS/3.meryl/"
LOOKUP_TABLE="/slurm/users/reference/lookup_table.txt"
MERFIN_OUTPUT=test
merfin -polish -sequence ${INPUT} -vcf ${MERGE_VCF_OUTPUT} -threads ${THREADS} -readmers ${READMER_DB} -prob ${LOOKUP_TABLE} -peak 10.8 -output ${MERFIN_OUTPUT}

In this section,

MERGE_VCF_OUTPUT is from medaka’s result “calls_to_draft.bam” and I transfer it to .vcf through samtools.

INPUT is from medaka’s result “consensus.fasta”.

READMER_DB is from NGS meryl

Is there any issues on my input data which causes wrong result?