Plugin error from Phylogeny 2022

User Support
#1

I know there are similar topics out there on this but none seemed to answer my question. I have run this code before and it works. I decided to run my data with DADA2 for denoising and then went on to the next step of creating a phylogenetic tree. I just ran it third time by creating a new directory for this analyses but got this same error again.

First the code I used: qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs.qza
--o-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
--o-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza

Error message:
Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/qd/kjfz98hs7ssch40klxyrpmd00000gn/T/qiime2-archive-p_xkk9qr/b27ae4da-ba4a-4741-9d5a-0b085082b7eb/data/dna-sequences.fasta']' returned non-zero exit status 1.

Debug info has been saved to /var/folders/qd/kjfz98hs7ssch40klxyrpmd00000gn/T/qiime2-q2cli-err-0nbfajgy.log

I have not done anything different this time around. Please help. Thanks!
Edit: I did use the RESCRIPT process to train my classification for taxonomic analyses. there might be an issue there?

#2

Hi @wendyhaeco,

Can you re-run this command using the --verbose flag, and then paste that output here?

Some thoughts:

  • How large is this data set?
    • You can run qiime feature-table tabulate-seqs... and qiime feature-table summarize ... to do this.
    • Often having no sequences, or too many sequences, can cause problems. If the latter, you have two options, filter your data to remove low-abundant features, or add the --p-parttree flag to your command.

Nope, you should be fine. Training the classifier is altogether a different set of steps using entirely different files.

#3

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