Bug with n_metagenome_reads


I hope you are doing well, Thank you fro your work on metaphan3. I think I found a bug

I use metaphan3 with the --nreads, --unknown_estimation and --input_type sam, I have the following error message:

fraction_mapped_reads = min(tot_nreads/float(n_metagenome_reads), 1.0) if ESTIMATE_UNK else 1.0
  TypeError: float() argument must be a string or a number, not 'NoneType'

I did a bit of digging in the code and found that the

Maybe pars[‘nreads’] should be used instead. This issue doesn’t occur when I omit the --unknown_estimation tag

Thank you for spotting this, I may have forgotten to specify to use the pars[‘nreads’] value when a SAM file is used as input. The latest commit fixes this.

Thank you very much! That was quick.

Hopefully the conda/singularity/docker container will be updated soon.