Jared Simpson comments

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                                            Jared Simpson

Error faidx could not get contig length for contig {1}

What is the exact error message that you got?

Error faidx could not get contig length for contig {1}

The `{1}` token is supposed to be replaced with the contig name by `parallel`. Perhaps there is a problem with how you're calling parallel?

Running 5 hours with the empty error.txt and empty .vcf output files.

Nanopolish variants is now largely deprecated, and you will likely get better results from medaka or clair3. This is especially true for R10.4.1 data, which nanopolish variants does not support....

nanopolish call-methylation showing Segmentation fault (core dumped)

Hi @shakti83kumar, It looks like you are trying to call rna modifications using recent (R10.4.1?) data, which nanopolish does not support. If this is the case, I suggest using dorado...

nanopolish call-methylation showing Segmentation fault (core dumped)

> How did you know Sir? In the screenshots you provided the directory said "Epitranscriptomics"

creating bam files for 6mA and 4mC

Hi, Yes, the modbam support only works for CpG methylation. If you need modbams for other modifications and contexts I recommend using ONT's callers (guppy/dorado/remora). Jared