"qiime diversity alpha-rarefaction": delimiter to call multiple metrics?

Dear Qiime community and developers,

How do I delimit multiple metrics properly in a calll to qiime diversity alpha-rarefaction?

This: (--p-metrics mcintosh_e,michaelis_menten_fit,shannon \) does not work but gives:

Plugin error from diversity:                                                                        │ands
                                                                                                    │ * later - ready to run R scripts
  'set' object has no attribute 'type'  

Any comment would be appreciated.

Thank you for developing and supporting Qiime.

Kind regards,


P.S: Whole call:

  qiime diversity alpha-rarefaction \
    --i-table "$trpth"/"${query_tab[$i]}" \
    --p-max-depth "${depth[$i]}" \
    --i-phylogeny "$trpth"/"${mptpth[$i]}" \
    --m-metadata-file "$trpth"/"${map_txt[$i]}" \
    --p-min-depth 1 \
    --p-metrics mcintosh_e,michaelis_menten_fit,shannon,faith_pd,menhinick,margalef,simpson_e,dominance,lladser_pe,ace,enspie,brillouin_d,singles,observed_otus,pielou_e,berger_parker_d,gini_index,chao1,doubles,goods_coverage,mcintosh_d,simpson,heip_e,robbins,fisher_alpha \
    --p-steps 100 \
    --p-iterations 10 \
    --o-visualization "$trpth"/"${tax_crv[$i]}" \
    --verbose 2>&1 | tee -a "$trpth"/"Zenodo/Qiime/122_18S_097_cl_tree_curves_log.txt"
1 Like
--p-metrics mcintosh_e \
--p-metrics michaelis_menten_fit \
--p-metrics shannon \
1 Like

Thank you very much - I appreciate it.


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