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?