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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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chunk_info -> Error in scan #75

Closed duceppemo closed 1 year ago

duceppemo commented 1 year ago

Hi, Not sure why but I keep having the following error using the chunk_info command on my reference genome:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  line 2 did not have 8 elements
Calls: generate.genome.chunks.information -> read.table -> scan
Execution halted

I don't get this error with the provided reference in the get_data_bacteria dataset. Do you have any idea why I'm getting this error? My reference is NZ_CP059443.1.

duceppemo commented 1 year ago

I re-downloaded the reference genome and it somehow fixed my problem. I ran a diff on the two files and nothing obvious pops out. Go figure. Problem solved. It would have been good to know what that file is causing problem.

touala commented 1 year ago

Hi @duceppemo,

Thank you for the feedback. This could be helpful to other users.

Alan