Hi,
running the following command:
qiime dada2 denoise-paired
--i-demultiplexed-seqs /home/user/Scrivania/Insalata/16S/paired-end-demux-deprim.qza
--p-trunc-len-f 298
--p-trunc-len-r 279
--o-representative-sequences /home/user/Scrivania/Insalata/16S/rep-seqs-dada2.qza
--o-table /home/user/Scrivania/Insalata/16S/table-dada2.qza
--o-denoising-stats /home/user/Scrivania/Insalata/16S/stats-dada2.qza
--p-n-threads 30
--verbose
I receive the following error:
(qiime2-2021.11) user@user:~$ cat /tmp/qiime2-q2cli-err-lllcws3i.log
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/tmpiph45vm3/forward /tmp/tmpiph45vm3/reverse /tmp/tmpiph45vm3/output.tsv.biom /tmp/tmpiph45vm3/track.tsv /tmp/tmpiph45vm3/filt_f /tmp/tmpiph45vm3/filt_r 298 279 0 0 2.0 2.0 2 12 independent consensus 1.0 30 1000000
R version 4.0.5 (2021-03-31)
Carico il pacchetto richiesto: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.7 / RcppParallel: 5.1.4
- Filtering ..
- Learning Error Rates
75394 total bases in 253 reads from 2 samples will be used for learning the error rates.
70587 total bases in 253 reads from 2 samples will be used for learning the error rates. - Denoise samples ..
.. - Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) :
Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
Esecuzione interrotta
Traceback (most recent call last):
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 266, in denoise_paired
run_commands([cmd])
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpiph45vm3/forward', '/tmp/tmpiph45vm3/reverse', '/tmp/tmpiph45vm3/output.tsv.biom', '/tmp/tmpiph45vm3/track.tsv', '/tmp/tmpiph45vm3/filt_f', '/tmp/tmpiph45vm3/filt_r', '298', '279', '0', '0', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '30', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/home/user/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, 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.
what can be the problem?
Thanks!