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How to index genome file for MethylDackel?

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

methyldackel indexing genome methylation
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updated by ATpoint ATpoint • written by harshraje19 • harshraje19

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

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written by GenoMax GenoMax

I already tried this step still same issue.

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written by harshraje19 • harshraje19

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
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written by GenoMax GenoMax

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?

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written by harshraje19 • harshraje19

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.

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written by ATpoint ATpoint

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