Need help with DADA2 error

[adixit]

Hi All,
I am running the DADA2 step for denoising in QIIME2-2-2019.4. I have 46 pair-ended samples. Here are the parameters I am using for this step,
time qiime dada2 denoise-paired
–verbose
–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 0
–p-trunc-len-r 0
–p-max-ee 2
–p-n-threads 0
–o-representative-sequences rep-seqs.qza
–o-table table.qza
–o-denoising-stats stats-dada2.qza
After running this I am getting the following error.

R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.1 / RcppParallel: 4.4.2

1. Filtering Error in sendMaster(try(lapply(X = S, FUN = FUN, …), silent = TRUE)) :
   write error, closing pipe to the master
   Error in names(answer) <- names1 :
   ‘names’ attribute [46] must be the same length as the vector [45]
   Execution halted
   Traceback (most recent call last):
   File “/home/titanadmin/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
   run_commands([cmd])
   File “/home/titanadmin/miniconda3/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/titanadmin/miniconda3/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/tmpiw3t2taf/forward’, ‘/tmp/tmpiw3t2taf/reverse’, ‘/tmp/tmpiw3t2taf/output.tsv.biom’, ‘/tmp/tmpiw3t2taf/track.tsv’, ‘/tmp/tmpiw3t2taf/filt_f’, ‘/tmp/tmpiw3t2taf/filt_r’, ‘0’, ‘0’, ‘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/titanadmin/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</home/titanadmin/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>”, line 2, in denoise_paired
File “/home/titanadmin/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/titanadmin/miniconda3/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/titanadmin/miniconda3/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.

Can someone please point me in the right direction.

Thank you all for your time.

[Mehrbod_Estaki]

Hi @adixit,
Welcome to the forum!
The --p-trunc-len changes @timanix suggested is not the issue here as your value of 0 there simply means no truncating is happening, so in essence it is in fact the maximum length you could have, therefore maximum overlap.

I think the important error is this:

@adixit

names’ attribute [46] must be the same length as the vector [45]

which according to a similar post here might be related to something going wrong with the core calculations. Can you try running your script again but manually put the # of threads in --p-n-threads instead of leaving it to be automatically detected?

[adixit]

Thank you very much. Specifying number of threads did the trick. Appreciated.