# DADA2 error for 18S paired end reads
**URL:** https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992
**Category:** User Support
**Tags:** dada2, 18s
**Created:** [November 24, 2024, 3:44pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992 "2024-11-24T15:44:31Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@nietof](https://forum.qiime2.org/u/nietof)
#### Post date: [November 24, 2024, 3:44pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992/1 "2024-11-24T15:44:31Z")
Hi
I have a similar problem. I am denoising 11 samples paired end reads for 18S amplicon. I am running the qiime2-amplicon-2024.5 installed natively in my macbook pro 2.3. GHz 8 core intel core i9 with 64GB RAM and 1TB hard disk. I am running it in the terminal.
Here is the demux.qzv:
[18S-demux.qzv](https://forum.qiime2.org/uploads/short-url/c3Yhp67j9o6obf0itgjIJpOPRri.qzv) (310.1 KB)
This is the command I am using for DADA2 denoising:
qiime dada2 denoise-paired
--i-demultiplexed-seqs 18S-demux-paired-end.qza
--p-trunc-len-f 0
--p-trunc-len-r 0
--p-n-threads 0
--o-table 18S-table.qza
--o-representative-sequences 18S-rep-seqs.qza
--o-denoising-stats 18S-stats.qza
--verbose
It has been running for 10 hours and 36 minutes.
Here is the R learning error rate:
3) Learning Error Rates
415177372 total bases in 2773272 reads from 1 samples will be used for learning the error rates.
This is the third time I tried running DADA2 and it the two previous cases gave me the same error as the one @Adyasha_Panda is getting, i.e. "An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more."
The previous times I didn't use the --verbose command so I can't tell where it got stuck and I don't know how to access the stdout and stderror logs.
I have also tried the denoising the samples using q2galaxy with the same result. I think in this case was a memory capacity issue.
Any help would be greatly appreciated.
Happy Thanksgiving
Fernando
---
### Author:  [@nietof](https://forum.qiime2.org/u/nietof)
#### Post date: [November 24, 2024, 3:47pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992/2 "2024-11-24T15:47:26Z")
BTW here are the processes going on right now:
Processes: 519 total, 3 running, 516 sleeping, 3161 threads 10:46:34
Load Avg: 6.84, 7.70, 7.62 CPU usage: 19.93% user, 1.81% sys, 78.25% idle
SharedLibs: 529M resident, 90M data, 54M linkedit.
MemRegions: 674003 total, 15G resident, 303M private, 2875M shared.
PhysMem: 52G used (4447M wired), 12G unused.
VM: 48T vsize, 2318M framework vsize, 0(0) swapins, 0(0) swapouts.
Networks: packets: 1034996/986M in, 857148/280M out.
Disks: 1731146/32G read, 837958/26G written.
PID COMMAND %CPU TIME #TH#WQ#PORT MEM PURG CMPRS PGRP
4637 R 306.3 03:18:28 17/1 0 293 6825M 0B 0B 4635
518 Finder 15.6 10:20.51 9 7 807 98M 136K 0B 518
155 WindowServer 8.8 21:27.83 27 17 1798- 356M- 2304K 0B 155
5641 top 8.6 03:13.04 1/1 0 39 4804K 0B 0B 5641
663 Spotify Help 6.8 13:01.76 41 1 313 156M 0B 0B 637
3769 Terminal 3.0 00:40.79 12 7 305+ 54M- 16M+ 0B 3769
0 kernel\_task 2.5 07:14.57 286/16 0 0 79M- 0B 0B 0
380 TouchBarServ 1.7 00:55.67 7 3 373+ 22M+ 2688K 0B 380
146 bluetoothd 0.8 00:21.95 4 2 205+ 4020K+ 0B 0B 146
468 Google Chrom 0.8 12:41.12 41 1 1177 302M 236K 0B 468
427 dorado\_basec 0.6 01:06.49 55 0 77 47M 0B 0B 109
2514 RdrCEF Helpe 0.2 00:15.69 9 1 193 40M 0B 0B 2509
564 Google Chrom 0.2 02:51.45 24 1 305+ 59M+ 0B 0B 468
542 sharingd 0.1 00:12.47 3 1 265 11M 1728K 0B 542
The R error process is using between 250 and 320% CPU. I have a feeling that is where the problem is.
Thank you again
Regards
Fernando
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [November 26, 2024, 7:46pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992/3 "2024-11-26T19:46:53Z")
Hello Fernando,
I think this may be a different issue, and if it is I'll split up these two threads to avoid bothering Adyasha.
> [@nietof](#):
>
> The R error process is using between 250 and 320% CPU. I have a feeling that is where the problem is.
That's good! That's means it's still running ⏳
> The previous times I didn't use the --verbose command so I can't tell where it got stuck and I don't know how to access the stdout and stderror logs.
If you do get the error again, then we will need to logs.
No logs -\> no clues -\> no idea! 🤷
From the terminal on your mac, try running
`open .`
If you were using WSL on Windows, the equlivent command is
`explorer.exe .`
That will open the current working directory so you can look at the files _without_ using Linux terminal commands.
---
### Author:  [@nietof](https://forum.qiime2.org/u/nietof)
#### Post date: [November 27, 2024, 1:44pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992/4 "2024-11-27T13:44:08Z")
GM @colinbrislawn
I hope all is welll with you today.
Following on this thread, the dada2 run ended with this error:
"\*R version 4.3.3 (2024-02-29) \*
_Loading required package: Rcpp_
\*DADA2: 1.30.0 / Rcpp: 1.0.12 / RcppParallel: 5.1.6 \*
_2) Filtering ..........._
_3) Learning Error Rates_
_415177372 total bases in 2773272 reads from 1 samples will be used for learning the error rates._
_open ._
\*Error in derepFastq(fls[[i]], qualityType = qualityType) : \*
- Not all provided files exist.\*
_5: stop("Not all provided files exist.")_
_4: derepFastq(fls[[i]], qualityType = qualityType)_
_3: learnErrors(filtsR, nreads = nreads.learn, multithread = multithread)_
\*2: withCallingHandlers(expr, warning = function(w) if (inherits(w, \*
-
```
classes)) tryInvokeRestart("muffleWarning"))*
```
_1: suppressWarnings(learnErrors(filtsR, nreads = nreads.learn, multithread = multithread))_
_Traceback (most recent call last):_
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2\_dada2/\_denoise.py", line 350, in denoise\_paired\*
- run\_commands([cmd])\*
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2\_dada2/\_denoise.py", line 37, in run\_commands\*
- subprocess.run(cmd, check=True)\*
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run\*
- raise CalledProcessError(retcode, process.args,\*
_subprocess.CalledProcessError: Command '['run\_dada.R', '--input\_directory', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/forward', '--input\_directory\_reverse', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/reverse', '--output\_path', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/output.tsv.biom', '--output\_track', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/track.tsv', '--filtered\_directory', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/filt\_f', '--filtered\_directory\_reverse', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/tmp9oibcr5r/filt\_r', '--truncation\_length', '0', '--truncation\_length\_reverse', '0', '--trim\_left', '0', '--trim\_left\_reverse', '0', '--max\_expected\_errors', '2.0', '--max\_expected\_errors\_reverse', '2.0', '--truncation\_quality\_score', '2', '--min\_overlap', '12', '--pooling\_method', 'independent', '--chimera\_method', 'consensus', '--min\_parental\_fold', '1.0', '--allow\_one\_off', 'False', '--num\_threads', '0', '--learn\_min\_reads', '1000000']' returned non-zero exit status 1._
_During handling of the above exception, another exception occurred:_
_Traceback (most recent call last):_
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in **call** \*
- results = self.\_execute\_action(\*
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in \_execute\_action\*
- results = action(\*_arguments)_
- File "", line 2, in denoise\_paired\*
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable\*
- outputs = self._callable\_executor_(\*
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in _callable\_executor_\*
- output\_views = self.\_callable(\*_view\_args)_
- File "/opt/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2\_dada2/\_denoise.py", line 363, in denoise\_paired\*
- raise Exception("An error was encountered while running DADA2"\*
_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."_
I don't know how to access the sdout and stderr files. I am not sure if this is the problem:
_5: stop("Not all provided files exist.")_
but I don't know what it means.
Thank you and Happy Thanksgiving.
Fernando
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 28, 2024, 10:24pm UTC](https://forum.qiime2.org/t/dada2-error-for-18s-paired-end-reads/31992/5 "2024-12-28T22:24:03Z")
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