Plugin error from diversity: Command '['faithpd'] returned non-zero exit status 1

When I use this script:
(qiime2-amplicon-2024.5) yixianbi@YixianBi:/mnt/c/qiime2bacteria$
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 42944
--m-metadata-file metadata.txt
--output-dir core-metrics-results

I obtained this error:
Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/yixianbi/data/570bbc50-f374-4689-9f27-a5a0b0e9a19d/data/feature-table.biom', '-t', '/tmp/qiime2/yixianbi/data/3ee16708-d40b-4a2d-b784-f2d0cc154adc/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-h77rdvp0']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-xeqh3qdp.log

The debug information as below:
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.


faithpd -i /tmp/qiime2/yixianbi/data/570bbc50-f374-4689-9f27-a5a0b0e9a19d/data/feature-table.biom -t /tmp/qiime2/yixianbi/data/3ee16708-d40b-4a2d-b784-f2d0cc154adc/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-h77rdvp0

Compute failed in faith_pd_one_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely).
Traceback (most recent call last):
File "/home/yixianbi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/", line 520, in call

And I tried use --verbose, it showed "--verbose: command not found".

I don't know why I got all of this. I have viewed all the topics but didn't find solutions.

Hello @Yixian_bi,

Welcome to the forums! :qiime2:

This is the core of the error:

This means that some feature/ASVs/OTUs in table.qza are not in rooted-tree.qza.

What's inside of rooted-tree.qza? This from a database or self-made?

1 Like

Thanks for your response.
I think the rooted-tree.qza is from a database. I just follow the tutorial pipeline step by step.
First, import 520 fastq.gz, output single-end-demux.qza;
Second, using DADA2, output table.qza and table.qzv;
Third, using alignment mafft to output aligned-rep-seqs.qza, using alignment mask to output masked-aligned-rep-seqs.qza, using phylogeny fasttree to output unrooted-tree.qza, and using phylogeny midpoint-root to output rood-tree.qza.

Did you use representative (your sequences, rep-seq.qza) or reference (from the database) sequences for rooted tree construction?
You should use representative sequences instead of reference.


1 Like

Thanks for your response. My script is as following:
time qiime alignment mafft
--i-sequences rep-seqs.qza
--p-n-threads 12
--o-alignment aligned-rep-seqs.qza

time qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza

time qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-n-threads 8 \
--o-tree unrooted-tree.qza

time qiime phylogeny midpoint-root \
--i-tree unrooted-tree.qza \
--o-rooted-tree rooted-tree.qza

I've used this pipeline for bacteria data several times, and only got error this time. I just update the qiime2 version from 2023.9 to 2024.5. I'm wondering if the error came from the qiime2 version?

Best regards,

1 Like

Commands look fine to me. You also used the rep-seqs file, and you already have some experience.
Did you filter your representative sequences separately from the table?

For sanity check, I would test it without: --p-parttree

Do you have 2023.9 still installed? Can you try it and report back?


1 Like