rescript edit-taxonomy error

Hi there!

I'm almost new qiime2 user. I'm trying to reach a good taxonomy classification for my analysis. I'm working with a classifier from gg training for the V3-V4 region... After some filtration process to remove unclassified sequences and all this stuff, I'm trying to rename some species (such as those classified as k__Bacteria; p__BRC1; c__PRR-11; o__; f__; g__; s__) with rescript edit-taxonomy. However qiimes gives me a warning: "c__PRR-11: command not found..."

Here is my script:
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

some help??

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

Hi!! I tried and it worked!! I also tried by a tsv file to change some names at the same time and it also worked using the whole entire string.

Thank you so much!!!

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:tada: I'm glad you got it to work! :raised_hands:

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