checkm coverage determins no mapped reads about checkm

[donovan-h-parks]

Hello,

By default, the CheckM coverage command only considered paired reads as these can be mapped with more confidence. However, using unpaired reads is supported you just need to pass the --all_reads flag.

Cheers,
Donovan

[jvollme]

Hi,
Thanks for the reply, but I did already try the "--all_reads" flag. Also I was under the impression that "-r" should be synonymeous to "--all_reads", based on the help text. But when that did not work, I tried the explicit "--all_reads" argument, to no avail.

[donovan-h-parks]

Sorry, '-r' and '--all_reads' are indeed the same. Didn't see that you were already throwing this flag. I'm not sure what the issue is. I use bwa for mapping reads so perhaps there is a difference between the BAM files produced by bwa and bowtie2. How large is your BAM file? If it isn't too large perhaps I can take a look at it to see if it works on my end.

[donovan-h-parks]

I am assuming this can be closed as there has been no follow-up in over a month.