# Plugin error from dada2:An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more
**URL:** https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292
**Category:** User Support
**Tags:** dada2
**Created:** [July 27, 2018, 2:31pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292 "2018-07-27T14:31:00Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@shixq](https://forum.qiime2.org/u/shixq)
#### Post date: [July 27, 2018, 2:31pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/1 "2018-07-27T14:31:00Z")
hi,I have been running dada2 on paired-end sequences, and it ran into a problem as following:
`Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and Debug info has been saved to /tmp/qiime2-q2cli-err-3jhw1xz_.log`
i have try to truncate any of low quality positions off of my reverse reads, and it does't work
##i gave the following command
2qiime dada2 denoise-paired
3 --i-demultiplexed-seqs paired-end-demux.qza
4 --p-trim-left-f 6
5 --p-trim-left-r 6
6 --p-trunc-len-f 130
7 --p-trunc-len-r 130
8 --o-table table.qza
9 --o-representative-sequences rep-seqs.qza
10 --o-denoising-stats denoising-stats.qza
#Debug log file
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/tmphkc9jaba/forward /tmp/tmphkc9jaba/reverse /tmp/tmphkc9jaba/output.tsv.biom /tmp/tmphkc9jaba/track.tsv /tmp/tmphkc9jaba/filt\_f /tmp/tmphkc9jaba/filt\_r 150 150 0 0 2.0 2 consensus 1.0 0 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 - 94912 reads in 40002 unique sequences.
Sample 2 - 139684 reads in 9861 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
selfConsist step 7
selfConsist step 8
selfConsist step 9
selfConsist step 10
Self-consistency loop terminated before convergence.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 94912 reads in 4862 unique sequences.
Sample 2 - 139684 reads in 10332 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 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/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 229, in denoise\_paired
run\_commands([cmd])
File "/home/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 36, in run\_commands
subprocess.run(cmd, check=True)
File "/home/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run\_dada\_paired.R', '/tmp/tmphkc9jaba/forward', '/tmp/tmphkc9jaba/reverse', '/tmp/tmphkc9jaba/output.tsv.biom', '/tmp/tmphkc9jaba/track.tsv', '/tmp/tmphkc9jaba/filt\_f', '/tmp/tmphkc9jaba/filt\_r', '150', '150', '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/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in **call**
results = action(\*\*arguments)
File "", line 2, in denoise\_paired
File "/home/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound\_callable
output\_types, provenance)
File "/home/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 366, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/home/shixq/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 244, 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.
#Additional information
It would be great if anyone could guide me.
The qiime 2 version that am using is qiime2 2018.6 and my i ran in linux(redhat)
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 27, 2018, 2:31pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/2 "2018-07-27T14:31:19Z")
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 30, 2018, 2:14pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/3 "2018-07-30T14:14:35Z")
Hi @shixq,
I don't think I've seen the chimera filtering step fail in that way before. I don't suppose you wouldn't be able to send a DM with your demultiplexed QZA file?
(pinging @benjjneb in case he's seen this before)
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 30, 2018, 2:14pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/4 "2018-07-30T14:14:38Z")
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 30, 2018, 2:43pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/5 "2018-07-30T14:43:59Z")
> [@ebolyen](#):
>
> I don’t think I’ve seen the chimera filtering step fail in that way before.
We have a handful of examples of this on the forum --- my understanding is this error happens when there are no SVs at this step --- usually an indication of insufficient overlap or incorrect trim/trunc params. @shixq - can you share your quality plots from the `demux summarize` command?
---
### Author:  [@shixq](https://forum.qiime2.org/u/shixq)
#### Post date: [July 30, 2018, 5:02pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/6 "2018-07-30T17:02:38Z")
@thermokarst, @ebolyen thanks a lot ，following is quality plots from the demux summarize command：
@thermokarst You are right, I just learned from squencing company that the overlap only 7-9bp, and I found some other topics in qiime2 forum which said a minimum of 20bp overlap was need for proper merging, is this correct？does it means the data can't be Processing in dada2? apart from deblur in qiime2, any suggestions for the analyse? @thermokarst, @ebolyen, thanks again!
Looking forward to hearing from you soon! -S
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 30, 2018, 5:16pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/7 "2018-07-30T17:16:18Z")
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 30, 2018, 7:48pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/8 "2018-07-30T19:48:23Z")
You should be able to use `denoise-single` instead in that case, as it will only consider the forward reads.
That being said, from the quality profile you've shared, those scores seem artificial. Is this data by chance from Mr. DNA?
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 30, 2018, 8:28pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/9 "2018-07-30T20:28:19Z")
---
### Author:  [@shixq](https://forum.qiime2.org/u/shixq)
#### Post date: [July 31, 2018, 12:54pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/10 "2018-07-31T12:54:46Z")
Hello! Thanks for the new command. I had tried denoise-single before, and it real worked, but isn't that reverse information lost, Is this a good choice? I got those two samples data from Sequencing company, how do I judge whether those scores are artificial data?
thanks for your patient！
shixq
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 31, 2018, 1:06pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/11 "2018-07-31T13:06:59Z")
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 2, 2018, 1:27pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/12 "2018-08-02T13:27:08Z")
> [@shixq](#):
>
> how do I judge whether those scores are artificial data
Check out [this post](https://forum.qiime2.org/t/interactive-quality-plot-colors/2990/13) for a good example of a "typical" Illumina run. When we see very uniform Q-score distributions, it is a pretty good indication that some kind of post-processing has occurred. Talk to your sequencing center and ask them for more details.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 2, 2018, 1:27pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/13 "2018-08-02T13:27:10Z")
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 2, 2018, 7:27pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/5292/14 "2018-09-02T19:27:15Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.