Hi, I've been having some troubles very similar to Error when running fastqPairedFilter · Issue #212 · benjjneb/dada2 · GitHub but the solution followed in this forum does not work for me.
I'm currently running Qiime2-2022.1 installed using conda.
I'm running dada2 with command:
qiime dada2 denoise-paired
--i-demultiplexed-seqs ./demux-paired-end.qza
--p-trunc-len-f 300
--p-trunc-len-r 240
--p-max-ee-r 12
--o-table demux-paired-end-table.qza
--o-representative-sequences demux-paired-end-rep-seqs.qza
--o-denoising-stats demux-paired-end-denoising-stats.qza
--p-n-threads 2
--verbose
And I get the error message:
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_paired.R /tmp/tmphxb4nupt/forward /tmp/tmphxb4nupt/reverse /tmp/tmphxb4nupt/output.tsv.biom /tmp/tmphxb4nupt/track.tsv /tmp/tmphxb4nupt/filt_f /tmp/tmphxb4nupt/filt_r 0 0 0 0 2.0 12 2 12 independent consensus 1.0 12 1000000
R version 4.1.3 (2022-03-10)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Execution halted
Traceback (most recent call last):
File "/home/keishamercy/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
run_commands([cmd])
File "/home/keishamercy/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/keishamercy/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmphxb4nupt/forward', '/tmp/tmphxb4nupt/reverse', '/tmp/tmphxb4nupt/output.tsv.biom', '/tmp/tmphxb4nupt/track.tsv', '/tmp/tmphxb4nupt/filt_f', '/tmp/tmphxb4nupt/filt_r', '0', '0', '0', '0', '2.0', '12', '2', '12', 'independent', 'consensus', '1.0', '12', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/keishamercy/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-45>", line 2, in denoise_paired
File "/home/keishamercy/miniconda3/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 "/home/keishamercy/miniconda3/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 "/home/keishamercy/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 292, in denoise_paired
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.
See above for debug info.
I've upgraded my R to the newest version, and also Qiime.
I've also tried installing the GenomeInfoDbData package in R. It should all be installed, but I still keep getting the same error message whenever I run the command. Is there anything else I can do to fix this?