ANCOM-BC plugin potential bug

Nicholas_Bokulich · December 17, 2021, 10:16am

I do not have a solution — I am only writing to highlight the information in this post from @jwdebelius :

and to say that

q2-ancombc appears to be still in development/incomplete, and ANCOM-BC is not developed or maintained by members of the Q2 team (otherwise we would be happy to help!)
I do not believe that the ANCOM-BC developers monitor this forum, and there is already a similar issue reported in the q2-ancombc github repository.
I do not think that the missing index in the biom table is actually the issue, because the error message appears to occur further downstream (i.e., after reading that table into R). I think the error might actually be indicating that the output file (list of features) is not formatted correctly.

You could try modifying the source code to uncomment this line:

mortonjt/q2-ancombc/blob/main/q2_ancombc/_method.py#L116


      
              # TODO: not sure what to do about the `global_test` statistic
              # may need another custom q2 type for this...
          except subprocess.CalledProcessError as e:
              raise Exception("An error was encountered while running ANCOMBC"
                              " in R (return code %d), please inspect stdout"
                              " and stderr to learn more." % e.returncode)
          
          summary = pd.read_csv(summary_fp, index_col=0)
          
          # del summary['diff_abn']  # remove this field for now ...
          summary.index.set_names("feature-id", inplace=True)
          return summary

A bit of a shot in the dark, but that's where I would begin.

Sorry that's not really an answer, just hoping to point you in the right direction and make it clear that I am not sure that this plugin is actually officially released yet