# Plugin error from dada2:R and Traceback
**URL:** https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985
**Category:** User Support
**Created:** [August 7, 2019, 1:25pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985 "2019-08-07T13:25:47Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 7, 2019, 1:25pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/1 "2019-08-07T13:25:47Z")
Hello!
I got the following error log when running quality control with DADA2:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--p-n-threads 3
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 280
--p-trunc-len-r 280
--o-table table-dada2.qza
--o-representative-sequences rep-seqs-dada2.qza
--o-denoising-stats denoising-stats-dada2.qza
**Here is the error log**
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 dep
Command: run\_dada\_paired.R /home/yuli/TMP\_Dir/tmpktpm35qo/forward /home/yuli/TMP\_Dir/tmpktpm3
R version 3.4.3 (2017-11-30)
Error: package ‘dada2’ was installed by an R version with different internals; it needs to be
Execution halted
Traceback (most recent call last):
File "/home/yuli/anaconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2\_dada2/\_denoise
run\_commands([cmd])
File "/home/yuli/anaconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2\_dada2/\_denoise
subprocess.run(cmd, check=True)
File "/home/yuli/anaconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in ru
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run\_dada\_paired.R', '/home/yuli/TMP\_Dir/tmpktpm35qo
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yuli/anaconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py
results = action(\*\*arguments)
File "\
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 7, 2019, 3:21pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/2 "2019-08-07T15:21:24Z")
I used the qiime2-2019.4 version, I think it may be the problem of R version?
I can run the whole process using the single end data and tutorials that from [https://docs.qiime2.org/2019.7/tutorials/fmt/](https://docs.qiime2.org/2019.7/tutorials/fmt/)，but it did not work when I use [this tutorials'](https://docs.qiime2.org/2019.7/tutorials/atacama-soils/) data and tutorials. It is so wired and bored me.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 7, 2019, 11:19pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/3 "2019-08-07T23:19:41Z")
Hi there @cyy!
> [@cyy](#):
>
> R version 3.4.3 (2017-11-30)
> Error: package ‘dada2’ was installed by an R version with different internals; it needs to be
This is not the version of R shipped with QIIME 2 - my guess is something in your environment is off, perhaps you have an `RPATH` value set? Please run the command `env` and return the results here. Thanks! 🦖
---
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 8, 2019, 3:17am UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/4 "2019-08-08T03:17:16Z")
Hi @thermokarst!
Thanks a lot! This is the result about running the env. [env.txt](https://forum.qiime2.org/uploads/short-url/oEuo03G9XNcmiFuuRPeoMjUjv4f.txt) (15.9 KB)
---
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 12, 2019, 2:14am UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/5 "2019-08-12T02:14:36Z")
Hi @thermokarst ！
Sorry about providing you the incomplete error log, and here is the complete log.[error log.txt](https://forum.qiime2.org/uploads/short-url/vIH6ep5o3tc7rHLNAbhq56d63X8.txt) (2.6 KB)
Thanks!😊
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 16, 2019, 4:00pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/6 "2019-08-16T16:00:28Z")
Thanks for sharing the `env` results --- I was looking for an `RPATH` variable, but didn't see one set (this is usually the guilty culprit here). One thing that did jump out at me is you `PATH`, which looks pretty jam-packed with things. Please run `which R` both before and after activating your QIIME 2 environment, and return the results here.
---
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 19, 2019, 2:15am UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/7 "2019-08-19T02:15:41Z")
Hi @thermokarst
Thanks a lot. I have update R to 3.6.1, and it could work at now.
There is another problem when I run the phylogeny plugin:
I notic that
"/home/yuli/lixs/software/prank/bin/mafft: line 1195: /home/yuli/lixs/software/pr
ank/bin/lib/replaceu: No such file or directory."
How can I solve it? Need I update the qiime2-2019.7?
Thanks again!
> Blockquote
> nseq = 2659
> nlen =
> distance = sixtuples
> iterate = 0
> cycle = 2
> /home/yuli/lixs/software/prank/bin/mafft: line 1195: /home/yuli/lixs/software/pr
> ank/bin/lib/replaceu: No such file or directory
> ED1lfnSh/pre: No such file or directory
> Traceback (most recent call last):
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cl
> i/commands.py”, line 327, in **call**
> results = action(\*\*arguments)
> File “\ orator.py:decorator-gen-477\>”, line 2, in mafft
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiim
> e2/sdk/action.py”, line 240, in bound\_callable
> output\_types, provenance)
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiim
> e2/sdk/action.py”, line 383, in _callable\_executor_
> output\_views = self.\_callable(\*\*view\_args)
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2\_a
> lignment/\_mafft.py”, line 85, in mafft
> run\_command(cmd, aligned\_fp)
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2\_alignment/\_mafft.py”, line 27, in run\_command
> subprocess.run(cmd, stdout=output\_f, check=True)
> File “/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
> output=stdout, stderr=stderr)
> subprocess.CalledProcessError: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘/home/yuli/TMP\_Dir/qiime2-archive-fmhs7exr/e1aa4400-1266
> -4faa-8ec0-13f5708dc2db/data/dna-sequences.fasta’]’ returned non-zero exit status 1.
---
### Author:  [@cyy](https://forum.qiime2.org/u/cyy)
#### Post date: [August 19, 2019, 1:54am UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/9 "2019-08-19T01:54:10Z")
Hi @colinbrislawn ,
I have some problem when running the phylogeny plugin. Please have a look the error log:
nseq = 2659
nlen =
distance = sixtuples
iterate = 0
cycle = 2
/home/yuli/lixs/software/prank/bin/mafft: line 1195: /home/yuli/lixs/software/pr
ank/bin/lib/replaceu: No such file or directory
ED1lfnSh/pre: No such file or directory
Traceback (most recent call last):
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cl
i/commands.py", line 327, in **call**
results = action(\*\*arguments)
File "\", line 2, in mafft
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiim
e2/sdk/action.py", line 240, in bound\_callable
output\_types, provenance)
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiim
e2/sdk/action.py", line 383, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2\_a
lignment/\_mafft.py", line 85, in mafft
run\_command(cmd, aligned\_fp)
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2\_alignment/\_mafft.py", line 27, in run\_command
subprocess.run(cmd, stdout=output\_f, check=True)
File "/home/yuli/anaconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/home/yuli/TMP\_Dir/qiime2-archive-fmhs7exr/e1aa4400-1266
-4faa-8ec0-13f5708dc2db/data/dna-sequences.fasta']' returned non-zero exit status 1.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [August 19, 2019, 4:31pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/10 "2019-08-19T16:31:33Z")
Here's the important part of the error:
```auto
/home/yuli/lixs/software/prank/bin/mafft: line 1195: /home/yuli/lixs/software/pr
ank/bin/lib/replaceu: No such file or directory
ED1lfnSh/pre: No such file or directory
```
Looks like either those directories don't exist, or you don't have permission to read/write to them.
Maybe they are misspelled? 🤷♂️
Let us know what you find!
Colin
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 19, 2019, 4:34pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/11 "2019-08-19T16:34:03Z")
@cyy --- this problem (
> [@cyy](#):
>
> /home/yuli/lixs/software/prank/bin/mafft: line 1195: /home/yuli/lixs/software/pr
> ank/bin/lib/replaceu: No such file or directory
)
appears to me to be another symptom of the same underlying issue - your `PATH` is likely inconsistent and causing all kinds of little issues like this.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 19, 2019, 10:34pm UTC](https://forum.qiime2.org/t/plugin-error-from-dada2-r-and-traceback/10985/12 "2019-09-19T22:34:04Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.