Plugin error from phylogeny

I received the following error when attempting to run this step from the moving pictures tutorial. Any help would be greatly appreciated.


qiime phylogeny fasttree \
  --i-alignment masked-aligned-rep-seqs.qza \
  --o-tree unrooted-tree.qza

Plugin error from phylogeny:
Command '['FastTree', '-nt', '/tmp/nes38/5129089/qiime2-archive-u16wlg
  sequences.fasta']' returned non-zero exit status 1

Hi @Nathan_Stone1, I need a little more information to figure out why this isn’t working. Can you please re-run the command with include the --verbose parameter, and then post the output in reply to this thread. This will cause a more detailed error message to be printed to the terminal.

This would look like the following:

qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree unrooted-tree.qza --verbose
FastTree: /lib64/ version `GLIBC_2.14' not found (required by FastTre$
Traceback (most recent call last):
  File "/packages/qiime2/2017.2.0/lib/python3.5/site-packages/q2cli-2017.2.0-py$
    results = action(**arguments)
  File "<decorator-gen-211>", line 2, in fasttree
  File "/packages/qiime2/2017.2.0/lib/python3.5/site-packages/qiime2-2017.2.0-p$
    output_types, provenance)
  File "/packages/qiime2/2017.2.0/lib/python3.5/site-packages/qiime2-2017.2.0-p$
    output_views = callable(**view_args)
  File "/packages/qiime2/2017.2.0/lib/python3.5/site-packages/q2_phylogeny-2017$
    run_command(cmd, tree_fp)
  File "/packages/qiime2/2017.2.0/lib/python3.5/site-packages/q2_phylogeny-2017$, stdout=output_f, check=True)
  File "/packages/qiime2/2017.2.0/lib/python3.5/", line 708, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['FastTree', '-nt', '/tmp/nes38/5129109$

Plugin error from phylogeny:

Thanks @Nathan_Stone1!

This seems to be an issue with the specific fasttree package that was installed on the system.

The following should generally work. This will uninstall the fasttree package that was installed from the biocore channel, and then install the package from the bioconda channel. It then re-installs q2-phylogeny, as that gets uninstalled with fasttree.

conda remove fasttree
conda install -c bioconda fasttree
conda install -c qiime2 q2-phylogeny

These commands were tested on a Linux system and solved the problem (incidentally, this is the same Linux system that @Nathan_Stone1 initially encountered the problem on, as we’re at the same institution).

1 Like

This solution works for me, but I’ve had to use it multiple times in version 2018.4. The error seems to be related to pulling up my QIIME1 environment while working in QIIME2, FYI.