error in qiime dada2 denoise-paired command

Hello Qiime2 team,
I am using qiime2-2019.10 and got the following error using qiime dada2 denoise-paired command:

*****below is complete error
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 245 --p-trunc-len-r 245 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 0 --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_paired.R /tmp/tmpcqewjq9m/forward /tmp/tmpcqewjq9m/reverse /tmp/tmpcqewjq9m/output.tsv.biom /tmp/tmpcqewjq9m/track.tsv /tmp/tmpcqewjq9m/filt_f /tmp/tmpcqewjq9m/filt_r 248 248 0 0 2.0 2.0 2 consensus 1.0 0 1000000

R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4

  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 :
    β€˜names’ attribute [104] must be the same length as the vector [102]
    Execution halted
    Traceback (most recent call last):
    File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/”, line 257, in denoise_paired
    File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/”, line 36, in run_commands, check=True)
    File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/”, line 418, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command β€˜[β€˜run_dada_paired.R’, β€˜/tmp/tmpcqewjq9m/forward’, β€˜/tmp/tmpcqewjq9m/reverse’, β€˜/tmp/tmpcqewjq9m/output.tsv.biom’, β€˜/tmp/tmpcqewjq9m/track.tsv’, β€˜/tmp/tmpcqewjq9m/filt_f’, β€˜/tmp/tmpcqewjq9m/filt_r’, β€˜248’, β€˜248’, β€˜0’, β€˜0’, β€˜2.0’, β€˜2.0’, β€˜2’, β€˜consensus’, β€˜1.0’, β€˜0’, β€˜1000000’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/”, line 328, in call
results = action(**arguments)
File β€œ</home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/>”, line 2, in denoise_paired
File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/”, line 240, in bound_callable
output_types, provenance)
File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/”, line 383, in callable_executor
output_views = self._callable(**view_args)
File β€œ/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/”, 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.

Please help me to solve this issue,
Thanks in advance,

Hi @khemlalnirmalkar,

I would suggest to switch to a more recent version of qiime if it is possible.
Still I would not expect this to fix your error, which is most likely a memory issue as discussed in: :sleeping:Denoising error, names attribute must be the same length as vector

That is, reducing the number of threads you are using should fix the problem!


This is the bulk of the error message, it is a bit cryptic, but it indicates that you have over-subscribed your host machine - you need to specify fewer threads when running q2-dada2.

1 Like

Yes, thanks @thermokarst @llenzi,
with fewer threads, it worked,