Failed to read fasta index (error 2)

[ramnageena11]

Pls look into this error and suggest how to resolve it?
Here:

1. I have indexed .bam (from dorado) and then converted to fasta (reads).
2. reference: assembled (genome: NCBI) or assembly from same long reads (using for modification analysis).

modkit pileup -t 4 --cpg --ref /home/Documents/......../genome_assemblies/bc01/ /home/Documents/demux-pod5/EXP-NBD104_barcode01.bam bc01.bed

calculated chunk size: 6, interval size 100000, processing 600000 positions concurrently
filtering to only CpG motifs
Error! Failed to read fasta index from "/home/Documents/genome_assemblies/bc01/.fai"
caused by No such file or directory (os error 2)

[ArtRand]

Hello @ramnageena11,

Could you try passing a path to the FASTA-formatted file containing the reference sequence? Something like /home/Documents/genome_assemblies/bc01/ref.fa, there needs to be an index as well such as /home/Documents/genome_assemblies/bc01/ref.fa.fai.