I read some previous posts about this error, but the log was slightly different and the suggestions weren’t helpful.
I used these instructions on QIIME1, to import some Roche454 data into QIIME2.
I successfully created a .qza file, then I tried to run denoise-pyro, as follows:
qiime dada2 denoise-pyro --i-demultiplexed-seqs /home/genomica/DATA/metagenomica/Bactrocera/sequenze/single_end.qza --p-trunc-len 0 --output-dir /home/genomica/DATA/metagenomica/Bactrocera/denoise --verbose
But that’s what I got:
(qiime2-2019.7) [genomica@localhost Bactrocera]$ qiime dada2 denoise-pyro --i-demultiplexed-seqs /home/genomica/DATA/metagenomica/Bactrocera/sequenze/single_end.qza --p-trunc-len 0 --output-dir /home/genomica/DATA/metagenomica/Bactrocera/denoise --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 /tmp/qiime2-archive-ng5mwdov/92863a33-b30f-47fa-8e93-2fe5e8a4d173/data /tmp/tmp0d53rpm6/output.tsv.biom /tmp/tmp0d53rpm6/track.tsv /tmp/tmp0d53rpm6 0 0 2.0 2 Inf consensus 1.0 1 250000 -1 32
R version 3.5.1 (2018-07-02)
Carico il pacchetto richiesto: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
1) Filtering Error in add(bin) : internal: buf != <newline>
Esecuzione interrotta
Traceback (most recent call last):
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 154, in _denoise_single
run_commands([cmd])
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-ng5mwdov/92863a33-b30f-47fa-8e93-2fe5e8a4d173/data', '/tmp/tmp0d53rpm6/output.tsv.biom', '/tmp/tmp0d53rpm6/track.tsv', '/tmp/tmp0d53rpm6', '0', '0', '2.0', '2', 'Inf', 'consensus', '1.0', '1', '250000', '-1', '32']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
results = action(**arguments)
File "</home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-461>", line 2, in denoise_pyro
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 274, in denoise_pyro
band_size='32')
File "/home/genomica/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 165, in _denoise_single
" and stderr to learn more." % e.returncode)
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.
What may be wrong there? Thanks in advance!
I’m using qiime2-2019.7