cutadapt in qiime2-2022.11

[lizgehret]

Hi @D_S,

Thanks for giving all of that a try. I suspect this is an issue with your virtual machine and how it's configured. Can you share exactly how you installed QIIME 2? Are you using Windows Subsystem for Linux (WSL) on this virtual machine?

[D_S]

Hi @lizgehret

Thanks for your continuous support.
Yes, after uninstalling the previous version of the QIIME2, I followed through these commands under the WSL - Natively installing QIIME 2 — QIIME 2 2023.5.1 documentation

wget https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
conda env create -n qiime2-2022.2 --file qiime2-2023.5-py38-linux-conda.yml
conda activate qiime2-2023.5

These are the details of the Hyper-V Manager I am using to acces the linux (Hyper-V-Manager,
Microsoft Corporation, Version: 10.0.19041.1)

Best,
Dharmesh

[lizgehret]

Hi @D_S,

Apologies for the delay. Are you using this virtual machine through your employer/institution? I'm wondering if this is due to a user permissions issue.

Cheers

[D_S]

Hi @lizgehret,

Thank you for your reply. I checked with the IT personnel here and there doesn't seem to be user permissions issue as there only a single login user id and pw and not different ones for admin and common users.

Also, I tried the denoise command (skipping the cutadapt) and it worked successfully:

qiime dada2 denoise-paired --i-demultiplexed-seqs seqs.qza --p-trim-left-f 18 --p-trim-left-r 21 --p-trunc-len-f 270 --p-trunc-len-r 250 --p-chimera-method consensus --p-min-fold-parent-over-abundance 4 --p-n-threads 36 --o-table table-denoise-seqs.qza --o-representative-sequences rep-denoise-seqs.qza --o-denoising-stats stats-denoise-seqs.qza

Since my forward and reverse primer lengths are 18 and 21 bps, I trimmed then using the p-trim-left- f & -r commands. Do you think I can skip the cutadapt steps and still receive the same output while using the trimming options in the denoising steps?

Best,
D_S

[lizgehret]

@D_S,

Thanks for following up with those details. There must be something strange happening with the actual cutadapt package that's installed on your machine. Can you run which cutadapt while in this same conda environment and copy/paste the results from your terminal in your response?

[D_S]

Hi @lizgehret ,

Thanks again for your support. I tried the command which cutadapt while in the same conda environment and below is the output:

/home/mih/ .local/bin/cutadapt

Best,
D_S

[lizgehret]

Hi @D_S,

Well that'll definitely do it - there does in fact seem to be a competing version of cutadapt on your machine, and that's almost certainly what's causing the issue here. I would remove this package, and then in your existing conda environment, run the following command:

conda install -c conda-forge -c bioconda cutadapt

This should resolve the issue, but go ahead and re-run which cutadapt afterwards to confirm that the path where this package exists is within your conda environment binaries. The path should look something like this:

/Users/username/miniconda3/envs/qiime2-2023.7/bin/cutadapt

Hope this helps! Cheers

[D_S]

Hi @lizgehret,

Thanks a lot for your suggestion.
I removed the competing version of cutadapt and rerunning which cutadapt yeilded the following output:

/home/mih/anaconda3/envs/qiime2-2023.5/bin/cutadapt.

This seemed correct and the cutadapt command within the conda qiime environment worked this time. Thanks a lot for your help and hopefully the subsequent steps will be completed without any errors..

Note: Since there was already a cutadapt within the qiime conda environment after removing the competing version, I did not run the following command:
conda install -c conda-forge -c bioconda cutadapt

Best,
D_S