rescript edit-taxonomy error

Community Plugin Support
2

Hi @Anuka,

I assume your intent is to replace this entire string:
p__BRC1; c__PRR-11; o__; f__; g__; s__
with this entire string:
p__ Incertae sedis; c__ Candidate; o__; f__; g__ Candidatus Sumerlaea; s__,

If so, then you need to place each in quotes as follows:

qiime rescript edit-taxonomy
    --i-taxonomy taxonomy.qza \
    --p-search-strings 'p__BRC1; c__PRR-11; o__; f__; g__; s__' \
    --p-replacements-strings 'p__Incertae sedis; c__Candidate; o__; f__; g_Candidatus Sumerlaea; s__chitinivorans' \
    --o-edited-taxonomy taxonomy-fixed.qza

Otherwise it will try and replace each search string (separated by a space) with its corresponding string in the replacement string list. That is 'p__BRC1; will be replaced by 'p__Incertae sedis;, and so on....

Note any taxonomic labels that contain spaces should be encapsulated in quotes. That is, if you really wanted to replace p__BRC1 with p__Incertae sedis and g__ with g__Candidatus Sumerlaea, then you'd enter the following:

  ...
    --p-search-strings 'p__BRC1' 'g__' \
    --p-replacements-strings 'p__Incertae sedis' 'g__Candidatus Sumerlaea' \
  ...

Give this a try and let us know if it works. :slight_smile:

-Mike