QIIME2 Galaxy Throwing Rcpp Loading Error

I was trying to perform DADA2-based denoising on a qza file and I received the following errror from QIIME2 Galaxy (cancer.usegalaxy.org/):

Loading required package: Rcpp
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/forward', '--input_directory_reverse', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/reverse', '--output_path', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/output.tsv.biom', '--output_track', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/track.tsv', '--filtered_directory', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/filt_f', '--filtered_directory_reverse', '/mnt/efs/fs1/cancer-usegalaxy-shared/database/jobs/019/19524/tmp7tymh0a3/filt_r', '--truncation_length', '225', '--truncation_length_reverse', '220', '--trim_left', '0', '--trim_left_reverse', '0', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000']' died with <Signals.SIGKILL: 9>.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/bin/q2galaxy", line 11, in
sys.exit(root())
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/main.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 30, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 115, in _execute_action
return action(**action_kwargs)
File "", line 2, in denoise_paired
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

Hey @macrobiome,

This error is typically due to a memory allocation issue - I haven't seen this come up using Galaxy before, but as a first step I'd recommend increasing your num_threads parameter to see if that resolves the issue.

Thanks @lizgehret! Is it possible to change the num_threads on Galaxy considering I am using the server hosted by a third party? (cancer.usegalaxy.org/)?

Hey @macrobiome, that's a good question - you are ultimately limited by what Galaxy has configured, but you could try increasing num_threads to something like 4, and that might not be unreasonable.

With that being said - if you are still unsuccessful, you may just not be able to run this command using Galaxy (since you are ultimately restricted in your memory allocation capabilities). It might be worth trying to utilize a native install of QIIME 2, if that's a feasible option for you on your machine.

Hope this helps, cheers :lizard:

Thank you! I forgot to mention that I had run this command previously and it worked. For some reason, it is not working anymore. I tried changing num_threads to both 0 and 4 but still getting the same error.

Hi @macrobiome,

Oh that's interesting - well in either case, there's not much that we can do directly to resolve this error since we aren't in control of that Galaxy server. If this is your only method for running QIIME 2, I'd say your next best bet would be to try and contact the IT admin for this Galaxy server and see if there's anything they can do (i.e. increase memory allocation, etc). Sorry we can't be of more help with this; best of luck! :lizard:

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