# Dada2 (return code 1)
**URL:** https://forum.qiime2.org/t/dada2-return-code-1/2972
**Category:** User Support
**Tags:** dada2
**Created:** [February 12, 2018, 9:04am UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972 "2018-02-12T09:04:10Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [February 12, 2018, 9:04am UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/1 "2018-02-12T09:04:10Z")
Hello,
I have received an error while running dada2. I run with --verbose and received these below:
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 /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/forward /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/reverse /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/output.tsv.biom /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt\_f /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt\_r 295 246 0 0 2.0 2 consensus 1.0 1 1000000
During startup - Warning messages:
1: Setting LC\_COLLATE failed, using "C"
2: Setting LC\_TIME failed, using "C"
3: Setting LC\_MESSAGES failed, using "C"
4: Setting LC\_MONETARY failed, using "C"
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1. Filtering Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 312, 313.
Execution halted
Traceback (most recent call last):
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 179, in denoise\_paired
run\_commands([cmd])
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 35, in run\_commands
subprocess.run(cmd, check=True)
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run\_dada\_paired.R', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/forward', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/reverse', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/output.tsv.biom', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt\_f', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt\_r', '295', '246', '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 "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in **call**
results = action(\*\*arguments)
File "", line 2, in denoise\_paired
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound\_callable
output\_types, provenance)
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 194, 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.
What could be the problem?
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [February 13, 2018, 12:16am UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/3 "2018-02-13T00:16:26Z")
Hi @Jewelna_Osei-Poku!
It looks like your original data has something wrong with it.
Could you run `qiime tools validate` on your `SampleData[SequencesWithQuality]` artifact (demux.qza)?
What was your import command also?
Thanks!
---
### Author:  [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [February 13, 2018, 2:47pm UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/5 "2018-02-13T14:47:22Z")
Thanks Evan for the response. Below was the message I had after running the qiime tools validate:
Artifact extracted\_with\_controls/metagseqs\_demux-paired-end.qza appears to be valid at level=max.
My import command is below:
qiime tools import --type "SampleData[PairedEndSequencesWithQuality]" --input-path extracted/metagseqs\_fastq --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path extracted/metagseqs\_demux-paired-end.qza
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [February 17, 2018, 12:43am UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/7 "2018-02-17T00:43:24Z")
Thanks @Jewelna_Osei-Poku,
So sorry for the slow response on my end!
It's a shame the `validate` didn't catch the issue ☹
Where did you get your original sequence files from? Was any filtering performed on it prior, if so, do you still have the raw-reads?
The issue is just that some reads are missing between your forward and reverse fastq files and that's confusing QIIME 2.
---
### Author:  [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [February 21, 2018, 11:45am UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/9 "2018-02-21T11:45:34Z")
Thanks Evan. You were absolutely right about the missing reads. Once I sorted that out the analyses worked fine.
Thanks you
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 24, 2018, 5:45pm UTC](https://forum.qiime2.org/t/dada2-return-code-1/2972/10 "2018-03-24T17:45:40Z")
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