Qiime2 DADA2 denoising error

Hi Guys,

I am getting a following error.
qiime dada2 denoise-paired --i-demultiplexed-seqs Combined.qza --p-trim-left-f 0 --p-trunc-len-f 260 --p-trim-left-r 0 --p-trunc-len-r 260 --o-representative-sequences trimmed-dada2.qza --o-table trimmed_table-dada2.qza --o-denoising-stats trimmed_stats-dada2.qza --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/tmpnnfv5q4c/forward /tmp/tmpnnfv5q4c/reverse /tmp/tmpnnfv5q4c/output.tsv.biom /tmp/tmpnnfv5q4c/track.tsv /tmp/tmpnnfv5q4c/filt_f /tmp/tmpnnfv5q4c/filt_r 260 260 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0

  1. Filtering …

  2. Learning Error Rates
    2a) Forward Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 13 reads in 9 unique sequences.
    Sample 2 - 13 reads in 10 unique sequences.
    selfConsist step 2
    Convergence after 2 rounds.
    2b) Reverse Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 13 reads in 13 unique sequences.
    Sample 2 - 13 reads in 13 unique sequences.
    selfConsist step 2
    Convergence after 2 rounds.

  3. Denoise remaining samples

  4. Remove chimeras (method = consensus)
    Error in isBimeraDenovoTable(unqs[[i]], …, verbose = verbose) :
    Input must be a valid sequence table.
    Calls: removeBimeraDenovo -> isBimeraDenovoTable
    In addition: Warning message:
    In is.na(colnames(unqs[[i]])) :
    is.na() applied to non-(list or vector) of type ‘NULL’
    Execution halted
    Traceback (most recent call last):
    File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
    run_commands([cmd])
    File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
    subprocess.run(cmd, check=True)
    File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpnnfv5q4c/forward’, ‘/tmp/tmpnnfv5q4c/reverse’, ‘/tmp/tmpnnfv5q4c/output.tsv.biom’, ‘/tmp/tmpnnfv5q4c/track.tsv’, ‘/tmp/tmpnnfv5q4c/filt_f’, ‘/tmp/tmpnnfv5q4c/filt_r’, ‘260’, ‘260’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>”, line 2, in denoise_paired
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/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.

Help me to fix this issue.
Thanks in advance.

By
Arun

Hi @arun_prasath!

We see this error when your reads are not able to be joined by DADA2. This usually means there is insufficient overlap with the settings provided for these reads.

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