How to index genome file for MethylDackel?

Question

[harshraje19]

I am running following script on my indexed and sorted bam file, but it is giving error on genome file. I indexed my genome file using both BWA index and samtools. (for both getting same error)

MethylDackel extract -@ 20 --chunkSize 30000000 \ --methylKit Genome/Cow.fasta C10_BWA_sorted.bam.bai

Error message,

Couldn't load the index for Genome/Cow.fasta, will attempt to build it.
Couldn't build the index for Genome/Cow.fasta! File corrupted?

Note : The file is not corrupted, I already used this file for mapping successfully.

Could you please help me to solve the issue?. How to index genome file for MethylDackel

Thanks, Harshraj

[GenoMax]

Build an index using samtools faidx Genome/Cow.fasta.

[harshraje19]

I already tried this step still same issue.

[GenoMax]

If you have a .fai index file then issue is likely that you are trying to provide a .bai input instead of the BAM file (if your original example command line is correct).

Can you try the following?

MethylDackel extract -@ 20 --chunkSize 30000000 --methylKit Genome/Cow.fasta C10_BWA_sorted.bam

[harshraje19]

Thank you GenoMax. I tried this and geting same error again.

Couldn't load the index for /Genome1/Cow.fasta, will attempt to build it. Couldn't build the index for /Genome1/Cow.fasta! File corrupted?

[ATpoint]

Is this the exact command line you used? Couldn't load the index for /Genome1/Cow.fasta Suggests that the /Genome folder is directly in the root directory which is unlikely. cd into the genome directory, type pwd and use the returned path.