Missing dependency pyrodigal in bioconda recipe/biocontainers

Microbial community profiling PhyloPhlAn
1

Hello everyone,

When trying to run phylophlan_assign_sgbs with the latest biocontainers image docker:// ``quay.io/biocontainers/phylophlan:3.2.1--pyhdfd78af_1, I get an error message that pyrodigal cannot be executed.

Traceback (most recent call last):
File “/usr/local/bin/phylophlan_assign_sgbs”, line 8, in
sys.exit(main())
~~~~^^
File “/usr/local/lib/python3.14/site-packages/phylophlan/phylophlan_assign_sgbs.py”, line 774, in main
phylophlan_assign_sgbs(args)
~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File “/usr/local/lib/python3.14/site-packages/phylophlan/phylophlan_assign_sgbs.py”, line 583, in phylophlan_assign_sgbs
check_dependencies()
~~~~~~~~~~~~~~~~~~^^
File “/usr/local/lib/python3.14/site-packages/phylophlan/phylophlan_assign_sgbs.py”, line 131, in check_dependencies
r = sp.run(shlex.split(cmd), capture_output=True)
File “/usr/local/lib/python3.14/subprocess.py”, line 554, in run
with Popen(*popenargs, **kwargs) as process:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/lib/python3.14/subprocess.py”, line 1038, in init
self._execute_child(args, executable, preexec_fn, close_fds,
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pass_fds, cwd, env,
^^^^^^^^^^^^^^^^^^^
…<5 lines>…
gid, gids, uid, umask,
^^^^^^^^^^^^^^^^^^^^^^
start_new_session, process_group)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/lib/python3.14/subprocess.py”, line 1989, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘prodigal’

In the bioconda recipe of PhyloPhlAn v3.2.1, pyrodigal is not listed as a dependency. I can execute phylophlan_assign_sgbs via conda after I additionally installed pyrodigal, too.

Is this behaviour expected or did I miss something here?

2

Hello Alex, thank you for reporting this.

Indeed, the new version of the SGBs assignment uses prodigal specifically for assigning a phylum label to very unknown SGBs.

It looks like we missed the prodigal dependency when packaging the version in bioconda, sorry. We’ll update and fix this in the next version. For the moment, as you already did, you can just add prodigal to the conda env before running phylophlan_assign_sgbs.

Thanks a lot for using PhyloPhlAn.

Regards,

Francesco