Hello All,
I have read the similar topic that has been posted before. But suggested solutions didn’t work for me, so creating this topic again.
The data is pair-ends. The samples amplified at the expected size (390bp). The qiime2 version is 2019.10.
Firstly, I had trimmed adapters from demultiplexed reads.
qiime cutadapt trim-paired
--i-demultiplexed-sequences demultiplexed-seqs.qza
--p-front-f GTGTGCCAGCMGCCGCGGTAA
--p-error-rate 0
--o-trimmed-sequences trimmed-seqs.qza
--verbose
qiime demux summarize
--i-data trimmed-seqs.qza
--o-visualization trimmed-seqs.qzv
Output visualizations are as follows.
Then, I used dada2 to denoise data:
qiime dada2 denoise-paired
--i-demultiplexed-seqs trimmed-seqs.qza
--p-trunc-len-f 240
--p-trunc-len-r 185
--p-n-threads 10
--o-table table-dada2.qza
--o-representative-sequences rep-seqs-dada2.qza
--o-denoising-stats denoising-stats-data2.qza
--verbose
Loading required package: Rcpp
Error in names(answer) <- names1 :
'names' attribute [75] must be the same length as the vector [68]
Execution halted
Traceback (most recent call last):
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp8aveqrj0/forward', '/tmp/tmp8aveqrj0/reverse', '/tmp/tmp8aveqrj0/output.tsv.biom', '/tmp/tmp8aveqrj0/track.tsv', '/tmp/tmp8aveqrj0/filt_f', '/tmp/tmp8aveqrj0/filt_r', '240', '185', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '10', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/share/apps/bio3user/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, in denoise_paired
" 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.
slurmstepd: error: Detected 1 oom-kill event(s) in step 19554325.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
I am really appreciated with your help.