Q2-fragment-insertion plugin reference tree issues

User Support
1

Hi guys,

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 \
--output-dir tutorial_placed_out

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 \
                                    --p-max-nsti 2

Thank you,
Barak

2

Hi @barakdror,

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.

Best,
Justine

3 Likes
3

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]?

Thank you,
Barak

4

Hey there @barakdror!

Not in QIIME 2. Do you not still have the original representative sequences on hand used to generate this FeatureData[AlignedSequence]?

5

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