# Qiime dada2 denoise-paired giving error **URL:** \ **Category:** User Support\ **Tags:** dada2, import\ **Created:** [July 19, 2018, 11:13am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116 "2018-07-19T11:13:06Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [July 19, 2018, 11:13am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/1 "2018-07-19T11:13:06Z")
I believe this topic has really been exhausted, please bare with me, I have Illumina ITS (1 and 4) Miseq paired end data and I received the sequences with barcodes removed and I then removed the illumina adapters and low quality reads using trimmomatic, so I tried removing primers using QIIME DADA2. I have attached a screenshot of what my sequences looked like prior oligos removal I then ran qiime dada2 denoise-paired --i-demultiplexed-seqs 1paired-end-demux.qza --p-trim-left-f 19 --p-trunc-len-f 300 --p-trim-left-r 20 --p-trunc-len-r 280 --o-representative-sequences unite-ver7-99-classifier-20.11.2016.qza --output-dir table-dada2.qza and I get this error Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more. Debug info has been saved to /var/tmp/pbs.1477438.sched01/qiime2-q2cli-err-n5\_abr\_f.log Kindly assist ![05](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/c/c969a0cedcf22b800020e82737c45470b16d8f54.png) ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 19, 2018, 12:56pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/2 "2018-07-19T12:56:46Z")
Hi there @kedi! > [@kedi](#): > > /var/tmp/pbs.1477438.sched01/qiime2-q2cli-err-n5\_abr\_f.log Can you please attach that file to this topic? If it doesn't exist anymore, please rerun your command above with the `--verbose` flag added in, and copy-and-paste the results here. Thanks! ---
**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [July 23, 2018, 7:49am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/3 "2018-07-23T07:49:21Z")
Hi Sorry for only getting back to you now, couldnt locate the err file, this is the error I got Traceback (most recent call last): File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 229, in denoise\_paired run\_commands([cmd]) File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2\_dada2/\_denoise.py", line 36, in run\_commands subprocess.run(cmd, check=True) File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run\_dada\_paired.R', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/forward', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/reverse', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/output.tsv.biom', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/track.tsv', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/filt\_f', '/var/tmp/pbs.1484090.sched01/tmpzb83710l/filt\_r', '300', '280', '19', '20', '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 "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 274, in **call** results = action(\*\*arguments) File "", line 2, in denoise\_paired File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound\_callable output\_types, provenance) File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 367, in _callable\_executor_ output\_views = self.\_callable(\*\*view\_args) File "/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/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. Thanks for your assistance ---
**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [July 23, 2018, 11:56am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/4 "2018-07-23T11:56:25Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 23, 2018, 3:34pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/5 "2018-07-23T15:34:37Z")
Hey there @kedi - it looks like the entire error log didn't make it into the post --- you should see something that looks like [this](https://forum.qiime2.org/t/an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stdout-and-stderr-to-learn-more/1938/5) when you run your command with the `--verbose` flag. When in doubt, copy _everything_ the command outputs. Thanks! ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 23, 2018, 3:34pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/6 "2018-07-23T15:34:39Z")
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**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [August 7, 2018, 8:37am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/7 "2018-08-07T08:37:05Z")
![57](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/e/e6cf3b91a408ec1fe316579e89cefa322d11279c.png) Hi Sorry for only responding now, I was out sampling. Regards ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 7, 2018, 1:28pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/8 "2018-08-07T13:28:52Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 7, 2018, 2:08pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/9 "2018-08-07T14:08:12Z")
Hi @kedi - did you run with the `--verbose` flag? That still looks like it is missing the main body of the traceback. ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 7, 2018, 2:08pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/10 "2018-08-07T14:08:16Z")
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**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [August 20, 2018, 10:54am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/11 "2018-08-20T10:54:00Z")
Hi @thermokast Thanks for your response, it turned out it was the issue of memory, tried to rectify the error, however it gives me the empty outputs thanks in advance for your assistance ---
**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [August 20, 2018, 3:09pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/12 "2018-08-20T15:09:26Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 21, 2018, 3:52am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/13 "2018-08-21T03:52:37Z")
Hey there @kedi --- I can't really say for sure what is happening without seeing the full (`--verbose`) output when running the failing command. Please copy-and-paste that here. Thanks! ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 21, 2018, 3:52am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/14 "2018-08-21T03:52:39Z")
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**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [August 21, 2018, 4:36pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/15 "2018-08-21T16:36:14Z")
[qiime2-q2cli-err-p7u4utv6.txt](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/f/fe7338e0c5d407901c048088589a338cc480f28c.txt) (2.6 KB) [qiime2-q2cli-err-p7u4utv6.txt](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/f/fe7338e0c5d407901c048088589a338cc480f28c.txt) (2.6 KB) Hi Please find the attached error ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 21, 2018, 5:03pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/16 "2018-08-21T17:03:44Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 21, 2018, 5:05pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/17 "2018-08-21T17:05:10Z")
Thanks @kedi! From the error log: > `Mismatched forward and reverse sequence files: 100000, 602.` At least one of your samples has significantly more forward reads than reverse reads. Did you demux these sequences yourself? If so, can you provide some detail on how? If they came to you demuxed, how did you import them? ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [August 21, 2018, 5:05pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/18 "2018-08-21T17:05:12Z")
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**Author:** ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)\ **Post date:** [August 22, 2018, 7:44am UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/19 "2018-08-22T07:44:01Z")
I did quality filtering using trimmomatric, then used qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path manifest --output-path paired-end-demux.qza --source-format PairedEndFastqManifestPhred3, to import then I proceeded to the dada2 denoise step ---
**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [August 22, 2018, 2:23pm UTC](https://forum.qiime2.org/t/qiime-dada2-denoise-paired-giving-error/5116/20 "2018-08-22T14:23:30Z")
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