Zero reads in index error

[setshabaTaukobong]

Good day, 
I am trying to detect base modifications but I keep getting a specific error.
I basecalled using the Promethion instrument and got multiple bam files.

I then merged these bam files using the following command:
samtools merge merged.bam *.bam

I then proceeded to sort and index the final file. From there I used the following command:
modkit pileup Final.bam pileup.bed --log-filepath pileup.log I however get this error: calculated chunk size: 6, interval size 100000, processing 600000 positions concurrently
attempting to sample 10042 reads
Error! zero reads found in bam index

Could I please get some assistance on how to solve this?
Thank you