Hi,
using this script to perform the beta-div: (qiime2-2023.7)
qiime diversity core-metrics-phylogenetic --i-phylogeny mafft-fasttree-output2/rooted_tree.qza --i-table table_dada2.qza --p-sampling-depth 10000 --m-metadata-file metadata.txt
--output-dir betadiv_10000
I obtained this error:
Plugin error from diversity:
[Errno 8] Exec format error: 'faithpd'
Debug info has been saved to /tmp/qiime2-q2cli-err-lyopx16_.log
Hi @Elnaz_Vjd96,
Can you please try re-running your command with the --verbose flag and copy/paste the results in your response? Thanks! 
Thanks for your reply.Here is the error:
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.
Command:
faithpd -i /tmp/qiime2/elnaz/data/554ae8fe-3670-421f-838c-afd9dba6da7f/data/feature-table.biom -t /tmp/qiime2/elnaz/data/3b91c674-7b36-4937-8d00-a491ba5c68d0/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-xd0xxp9i
Traceback (most recent call last):
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 544, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 62, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 69, in _disallow_empty_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 112, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 128, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 122, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 493, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/elnaz/miniconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 8] Exec format error: 'faithpd'
Plugin error from diversity:
[Errno 8] Exec format error: 'faithpd'
See above for debug info.
Hello @Elnaz_Vjd96. Can you activate your conda environment and run the command faithpd in it and post the result here?
I tried this and here it is the error:
(qiime2-2023.7) elnaz@Elizabeth:~$ qiime faithpd
Error: QIIME 2 has no plugin/command named 'faithpd'.
Hi @Elnaz_Vjd96, You should not include qiime in that command (i.e., it should be faithpd, not qiime faithpd).
I have the same issue and when i run faithpd i get the following:
bash: /home/nuranwar/anaconda3/envs/qiime2/bin/faithpd: cannot execute binary file: Exec format error
Hello @nur (and if you get the same error when running faithpd on its own @Elnaz_Vjd96), the error @nur is getting means you have the incorrect faithpd binary. Are you sure you followed the correct install instructions on this page based on your operating system?
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