Hello,
I've been encountering a problem after the denoising step with DADA2:
DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Here's the run with --verbose:
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_single.R /var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-bexar_aw /var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw/output.tsv.biom /var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw/track.tsv /var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw 150 0 2.0 2 Inf independent consensus 1.0 1 1000000 NULL 16
R version 4.1.3 (2022-03-10)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/R/library/png/libs/png.dylib':
dlopen(/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/R/library/png/libs/png.dylib, 6): Library not loaded: @rpath/libpng16.16.dylib
Referenced from: /Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/R/library/png/libs/png.dylib
Reason: Incompatible library version: png.dylib requires version 55.0.0 or later, but libpng16.16.dylib provides version 54.0.0
Execution halted
Traceback (most recent call last):
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 195, in _denoise_single
run_commands([cmd])
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-bexar_aw', '/var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw/output.tsv.biom', '/var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw/track.tsv', '/var/folders/73/ggsnhrqd6678b3bzfkv9bvlc0000gn/T/tmp1n1m6xpw', '150', '0', '2.0', '2', 'Inf', 'independent', 'consensus', '1.0', '1', '1000000', 'NULL', '16']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 218, in denoise_single
return _denoise_single(
File "/Users/kotasuzuki/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 204, in _denoise_single
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I've checked other forums regarding the same error message, but I don't think it's because the forward and reverse reads are identical or a thread issue. I tried running the same code with --p-n-threads 1 and no --p-n threads command at all and I still ran into the issue. I checked the .qzv file on qiime2view and the study looks fine in terms of the forward and reverse reads being identical.
Any help/insight would be greatly appreciated!