# Cut adapt results in empty files
**URL:** https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678
**Category:** User Support
**Tags:** cutadapt
**Created:** [October 18, 2024, 5:57pm UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678 "2024-10-18T17:57:05Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@tinoracha](https://forum.qiime2.org/u/tinoracha)
#### Post date: [October 18, 2024, 5:57pm UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678/1 "2024-10-18T17:57:05Z")
I am follwing the [PacBio CCS Amplicon SOP v1](https://github.com/LangilleLab/microbiome_helper/wiki/PacBio-CCS-Amplicon-SOP-v1-(qiime2)) for Qimme2 and I can't seem to get cut adapt to work. The command runs but the output files are empty, the naming + location is correct.
Input:
mkdir trimmed\_reads/
parallel -j 4 'cutadapt -g AGRGTTTGATCMTGGCTCAG...TACGGYTACCTTGTTACGACTT
--discard-untrimmed --no-indels -j 1 -m 1200 -M 1800
-o trimmed\_reads/{/.}\_trim.fastq {}'
::: raw\_data\_cat/\*\_cat.fastq
Output:
=== Adapter 1 ===
Sequence: TACGGYTACCTTGTTACGACTT...AGRGTTTGATCMTGGCTCAG; Type: linked; Length: 22+20; 5' trimmed: 0 times; 3' trimmed: 0 times
This is cutadapt 4.9 with Python 3.9.19
Command line parameters: -g TACGGYTACCTTGTTACGACTT...AGRGTTTGATCMTGGCTCAG --discard-untrimmed --no-indels -j 1 -m 1200 -M 1800 -o trimmed\_reads/2314\_16S\_02\_SD\_2.49\_388\_cat\_trim.fastq raw\_data\_cat/2314\_16S\_02\_SD\_2.49\_388\_cat.fastq
Processing single-end reads on 1 core ...
Finished in 1.325 s (26.286 µs/read; 2.28 M reads/minute).
=== Summary ===
Total reads processed: 50,424
Reads with adapters: 0 (0.0%)
== Read fate breakdown ==
Reads that were too short: 52 (0.1%)
Reads that were too long: 0 (0.0%)
Reads written (passing filters): 0 (0.0%)
Total basepairs processed: 75,624,156 bp
Total written (filtered): 0 bp (0.0%)
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### Author:  [@tinoracha](https://forum.qiime2.org/u/tinoracha)
#### Post date: [October 18, 2024, 8:57pm UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678/2 "2024-10-18T20:57:38Z")
I've also been sent this message from the sequencing facility but I do not understand how to incorporate this into my code: "There are not adapters in the data. The data only has primer sequences. The adapters are removed during demultiplexing. I would suggest not using cutadapt for primer trimming as well. Within your cutadapt you are using –p-adapter twice whereas the data is single ended. If you want to continue using cutadapt, I suggest putting … between forward and reverse primer – like --p-adapter AGRGTTTGATCMTGGCTCAG…TACGGYTACCTTGTTACGACTT. That way cutadapt knows it must look for both the primers in the same single ended sequence. Within qiime dada2 denoise-ccs there is an option to specify –p-front parameter (forward primer) and –p-adapter (reverse primer). You can directly use that to remove primers and denoise the data."
Thank you!
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [October 18, 2024, 9:13pm UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678/3 "2024-10-18T21:13:00Z")
Hello Tino,
Thank you for bringing this question to the forums!
First, I want to clarify that the SOP is from the LangilleLab [Langille Lab · GitHub](https://github.com/LangilleLab)
I can still help out with the Qiime2 part and offer some general advice.
> [@tinoracha](#):
>
> I can't seem to get cut adapt to work.
I concur with the advice from the sequencing core:
> [@tinoracha](#):
>
> There are not adapters in the data. The data only has primer sequences. The adapters are removed during demultiplexing. I would suggest not using cutadapt for primer trimming as well.
You can skip this step!
You can also do basic read trimming with DADA2, as mentioned here:
> [@tinoracha](#):
>
> Within qiime dada2 denoise-ccs there is an option to specify –p-front parameter (forward primer) and –p-adapter (reverse primer). You can directly use that to remove primers and denoise the data."
Here is the documentation for `qiime dada2 denoise-ccs` so you can learn more:
[https://docs.qiime2.org/2024.5/plugins/available/dada2/denoise-ccs/](https://docs.qiime2.org/2024.5/plugins/available/dada2/denoise-ccs/)
---
### Author:  [@tinoracha](https://forum.qiime2.org/u/tinoracha)
#### Post date: [October 18, 2024, 9:16pm UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678/4 "2024-10-18T21:16:21Z")
Hey Colin, Thanks so much for the reply. Sounds like going through denoising will do the trick for me.
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 19, 2024, 3:16am UTC](https://forum.qiime2.org/t/cut-adapt-results-in-empty-files/31678/5 "2024-11-19T03:16:49Z")
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