I’m having some difficulties while trying to run the PICRUST2 plugin (qiime 2018.6).
I understand that before running the full PICRUST pipeline, I need to run the q2-fragment-insertion. However, when trying to do so with my own rep-seqs:
qiime fragment-insertion sepp
--i-representative-sequences aligned_seqs.qza \
--p-threads 1 --i-reference-alignment reference.fna.qza \
--i-reference-phylogeny reference.tre.qza \
I’m getting this error:
Error: No such command “fragment-insertion”
How should I handle this issue? is this actually what I should do before moving into this step:
qiime picrust2 custom-tree-pipeline --i-table mammal_biom.qza \
--i-tree tutorial_placed_out/tree.qza \
--output-dir q2-picrust2_output \
--p-threads 1 --p-hsp-method pic \
For QIIME releases prior to 2018.11, you need to install fragment-insertion plug in separately. If you don’t have it installed, I would start there.
Thank you, I updated to version 2018.11 and now I can find the fragment-insertion command.
However, now that I’m trying to use it, it seems that it can’t accept aligned sequences as input, but only FeatureData[Sequence]:
> qiime fragment-insertion sepp \
> --i-representative-sequences aligned_seqs.qza \
> --p-threads 10 \
> --i-reference-alignment reference.fna.qza \
> --i-reference-phylogeny reference.tre.qza \
> --output-dir insertion_test
Since I got these data from third party, is there a way to convert FeatureData[AlignedSequence] to FeatureData[Sequence]?
Hey there @barakdror!
Not in QIIME 2. Do you not still have the original representative sequences on hand used to generate this
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.