Dear whom it may concern:
I want to obtain the 6mA methylation modification of the genome through the fast5 file of ONT sequencing. The first thing I needed to fix was that the fast5 file from the sequencing company doesn't have the events table. So I need to rebasecalling with Guppy software, but I found that it no longer supported the --fast_out on parameter, which means I couldn't use Guppy to write events tables to fast5 files.
Unexpected token '--fast5_out' on command-line.
I didn't find out much about this parameter, so I want to see what happens if I don't add this parameter. And then there's the second problem, which is that it takes so much time, When I converted mutil-fast5 to single-fast5 files, I produced 36 directories with a total of millions of fast5 files. I don't know how much time it will take to basecalling these files, but there are no results yet. I think there should be some problems with my progress, but I am not sure what is the right. Does anyone know what I should do next?
It would help if you provide the version of Guppy you are using.
Also as a side note, I would recommend switching to Dorado (https://github.com/nanoporetech/dorado)