# error while running qiime cutadapt trim-paired

**URL:** https://forum.qiime2.org/t/error-while-running-qiime-cutadapt-trim-paired/28627
**Category:** Technical Support
**Created:** [December 15, 2023, 11:10pm UTC](https://forum.qiime2.org/t/error-while-running-qiime-cutadapt-trim-paired/28627 "2023-12-15T23:10:50Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![Junli\_Zhang](https://forum.qiime2.org/user_avatar/forum.qiime2.org/junli_zhang/32/10122_2.png) [@Junli\_Zhang](https://forum.qiime2.org/u/Junli_Zhang)
#### Post date: [December 15, 2023, 11:10pm UTC](https://forum.qiime2.org/t/error-while-running-qiime-cutadapt-trim-paired/28627/1 "2023-12-15T23:10:51Z")

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Hi, I am trying to using cutadapt to trim the primers of the reads.  
below is the script I ran.  
qiime cutadapt trim-paired   
--i-demultiplexed-sequences pair-end-demux.qza   
--p-adapter-f GTTATTGTGATGTAGTTCCTG GTCGTTTTTGATCTGACAGG   
--p-front-f CCTGTCAGATCAAAAACGAC CAGGAACTACATCACAATAAC  
--p-adapter-r GTTATTGTGATGTAGTTCCTG GTCGTTTTTGATCTGACAGG   
--p-front-r CCTGTCAGATCAAAAACGAC CAGGAACTACATCACAATAAC  
--p-overlap 3   
--p-error-rate 0.1   
--p-match-read-wildcards   
--p-match-adapter-wildcards   
--p-minimum-length 1   
--p-discard-untrimmed   
--o-trimmed-sequences primer-trimmed-demux.qza   
However, I got this error.

Plugin error from cutadapt:

Command '['cutadapt', '--cores', '1', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-q', '0,0', '--quality-base', '33', '-o', '/scratch/local/18008173/q2-CasavaOneEightSingleLanePerSampleDirFmt-4dvpif7\_/cAE1-H\_0\_L001\_R1\_001.fastq.gz', '-p', '/scratch/local/18008173/q2-CasavaOneEightSingleLanePerSampleDirFmt-4dvpif7\_/cAE1-H\_9\_L001\_R2\_001.fastq.gz', '--adapter', 'GTTATTGTGATGTAGTTCCTG', '--adapter', 'GTCGTTTTTGATCTGACAGG', '--front', 'CCTGTCAGATCAAAAACGAC', '--front', 'CAGGAACTACATCACAATAAC--p-adapter-r', '--front', 'GTTATTGTGATGTAGTTCCTG', '--front', 'GTCGTTTTTGATCTGACAGG', '-G', 'CCTGTCAGATCAAAAACGAC', '-G', 'CAGGAACTACATCACAATAAC--p-overlap', '-G', '3', '--match-read-wildcards', '--discard-untrimmed', '/scratch/local/18008173/qiime2/zjl1983/data/a979e63a-e044-4b35-bff0-1f8a16e452da/data/cAE1-H\_0\_L001\_R1\_001.fastq.gz', '/scratch/local/18008173/qiime2/zjl1983/data/a979e63a-e044-4b35-bff0-1f8a16e452da/data/cAE1-H\_9\_L001\_R2\_001.fastq.gz']' returned non-zero exit status 2.

Could anyone help me to find out what the problem is? And How to solve it?

Thank you!

Junli

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### Author: ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [December 15, 2023, 11:11pm UTC](https://forum.qiime2.org/t/error-while-running-qiime-cutadapt-trim-paired/28627/2 "2023-12-15T23:11:58Z")

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Hi @Junli_Zhang,

Can you please re-run your command with the `--verbose` flag, and copy/paste the entire terminal output in your response? Thanks! 🦎

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [January 16, 2024, 5:12am UTC](https://forum.qiime2.org/t/error-while-running-qiime-cutadapt-trim-paired/28627/3 "2024-01-16T05:12:32Z")

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