dada2 denoise-paired error (running DADA2 in R return code 1)

[omomo]

Hello,everyone!

I have two series of data to process. One worked well and successfully I got rep-seqs.qza and table.qza by dada2 denosie-paired.

The code is as follows:

qiime dada2 denoise-paired
--i-demultiplexed-seqs ./one/paired-end-demux.qza
--p-n-threads 0
--p-trunc-len-f 140
--p-trunc-len-r 140
--o-table ./one/table.qza
--o-representative-sequences ./one/rep-seqs.qza
--o-denoising-stats ./one/denoising-stats.qza

While another(the same workflow, data size is more bigger than the success one) got error:

Loading required package: Rcpp
Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Execution halted
Traceback (most recent call last):
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp1_dt0jgq/forward', '/tmp/tmp1_dt0jgq/reverse', '/tmp/tmp1_dt0jgq/output.tsv.biom', '/tmp/tmp1_dt0jgq/track.tsv', '/tmp/tmp1_dt0jgq/filt_f', '/tmp/tmp1_dt0jgq/filt_r', '140', '140', '0', '0', '2.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>", line 2, in denoise_paired
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 246, 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.

My data is PE150, and target PCR region is 250bp, so I think trunc-len 140 is long enough for paried-joining.

What`s wrong ? Thanks a lot!!!!

[thermokarst]

Hey there @omomo!

Sorry for the slow reply!

This is the part of the error message that jumped out at me:

@omomo

Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Execution halted

We see this happen when you specify too many n-threads when running q2-dada2 - which lines up with your comment that this dataset is larger than the last successful one you ran, and also you're specifying 0 threads, which q2-dada2 translates to mean "run as many threads as possible."

You'll need to experiment with setting this to a lower value - I can't tell you what that value is, but maybe start with 8. If it fails with the same message, try 4.

Keep us posted!

[omomo]

Sorry for late reply ... Thanks a lot!!
It`s navie to think that if my data is bigger so I need more threads...

I will try less threads and I`ll post it as soon as if it works.