Hi there,
I know this is a topic that has been discussed a few times. I went through all the previous discussions and tried the suggestions. However, I am not able to figure out the problem. I have contacted our IT personnel to check if I have permission, and it looks like I have permission to write. I am hoping that you might be able to figure out anything that we missed.
I didn't have any problem running QIIME2 until core diversity metrics. here's the error message I got last time I ran the command.
qiime diversity core-metrics-phylogenetic \
--i-phylogeny phylogeny-align-to-tree-mafft-fasttree-positive/rooted_tree.qza
--i-table positive-filtered-table.qza
--p-sampling-depth 10
--m-metadata-file metadata.txt
--output-dir diversity-core-metrics-phylogenetic
--verbose
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Traceback (most recent call last):
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/util.py", line 486, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 90, in load
raise e
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 80, in load
archiver = archive.Archiver.load(filepath)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/archive/archiver.py", line 369, in load
cache._rename_to_data(archive.uuid, path)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/cache.py", line 1158, in _rename_to_data
os.rename(src, dest)
PermissionError: [Errno 13] Permission denied: '/tmp/qiime2/nilumal/processes/1707-1719245475.64@nilumal/fb48181c-9b20-4528-8bb6-cccf7d9c43df.6683109781917317288/fb48181c-9b20-4528-8bb6-cccf7d9c43df' -> '/tmp/qiime2/nilumal/data/fb48181c-9b20-4528-8bb6-cccf7d9c43df'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/click/type.py", line 116, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/util.py", line 391, in _load_input
artifact, error = _load_input_file(fp)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/util.py", line 492, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'Phylogeny[Rooted]' and format 'NewickDirectoryFormat'
There was a problem loading 'phylogeny-align-to-tree-mafft-fasttree-positive/rooted_tree.qza' as an artifact:
It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'Phylogeny[Rooted]' and format 'NewickDirectoryFormat'
See above for debug info.
I checked the following forum discussions and followed your suggestions.
Thanks for going through this @cherman2. I am running QIIME2 on my computer. Please check if this is what you wanted me to run.
qiime tools list-formats --exportable
NewickDirectoryFormat
No description
qiime tools list-formats --importable
NewickDirectoryFormat
No description
qiime tools list-types --strict
Phylogeny[Rooted]
A phylogenetic tree containing a defined root.
Can you tell me how you installed this?
Hi @cherman2, I figured I didn't answer all your questions. I have a Windows system with Ubuntu installed in it. I followed the installation for WSL on the tutorial. Do you think it might be good to remove Qiime 2 and re-install it? Thanks!
This is the error message after re-installing QIIME2
qiime diversity core-metrics-phylogenetic \
--i-phylogeny phylogeny-align-to-tree-mafft-fasttree-positive/rooted_tree.qza
--i-table positive-filtered-table.qza
--p-sampling-depth 10
--m-metadata-file metadata.txt
--output-dir diversity-core-metrics-phylogenetic
--verbose
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
warn(f"{func.name} is deprecated as of {ver}.")
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/skbio/_methods.py:71: RuntimeWarning: invalid value encountered in scalar divide
return _shannon(counts, base=np.e) / np.log(
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.5279235539366622 and the largest is 9.629056654170732.
warn(
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.970591151953257 and the largest is 10.60210398819732.
warn(
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.
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd: line 43: /home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd_nv_avx2: cannot execute binary file: Exec format error
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd: line 43: /home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd_nv_avx2: Success
Traceback (most recent call last):
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 657, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_core_metrics.py", line 65, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "", line 2, in faith_pd
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/alpha.py", line 63, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/nilumal/data/4168eb98-7787-4013-9cd2-92ec7c327819/data/feature-table.biom', '-t', '/tmp/qiime2/nilumal/data/fb48181c-9b20-4528-8bb6-cccf7d9c43df/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-dbyfzjxz']' returned non-zero exit status 126.
Plugin error from diversity:
Command '['faithpd', '-i', '/tmp/qiime2/nilumal/data/4168eb98-7787-4013-9cd2-92ec7c327819/data/feature-table.biom', '-t', '/tmp/qiime2/nilumal/data/fb48181c-9b20-4528-8bb6-cccf7d9c43df/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-dbyfzjxz']' returned non-zero exit status 126.
See above for debug info.
I saw a forum discussion related to Plugin error from diversity faithpd
When I run faithpd, here's what I get.
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd: line 43: /home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd_nv_avx2: cannot execute binary file: Exec format error
/home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd: line 43: /home/nilumal/miniconda3/envs/qiime2-amplicon-2024.5/bin/faithpd_nv_avx2: Success
What do you think is happening with my installation?
Thank you!
