cutadapt error "command not recognized"

Question

[KD]

Hi, I am facing trouble in running cutadapt command: I installed cutadapt and activated through conda, but when I am running my command: cutadapt -a ACTCCTACGGGAGGCAGCAG -o output.fastq input.fastq but it is showing error that "cutadapt" is not recognized command. I have tried to update variable path also but still its not working. Could you please help me out? I added cutadapt as new channel in anaconda, as it was not available earlier. Thank you

[Mark]

Find out where it was installed and reference it explicitly. eg: /home/bin/cutadapt1.2.3/cutadapt -a ACTCCTACGGGAGGCAGCAG -o output.fastq input.fastq

[ATpoint]

It means that your command is not in PATH. Please google what PATH is and how to set it up, that is basic Linux/Unix.

[Mark]

Yes that is true. But a workaround is just to specify the path. There's something else going on because KD uses conda and it handles PATH variables etc for you.

[ATpoint]

What does activated through conda mean? Did you make a new enviromnent for it? Are you sure you indeed pulled it to that environment rather that the base? Please show full installation commands.

[KD]

It was not in channels and asked to add in channel. then I added accordingly

conda create -n cutadapt python = 3.8

and it was installed 


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/win-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/win-64::certifi-2019.9.11-py37_0
  openssl            pkgs/main/win-64::openssl-1.1.1d-he774522_3
  pip                pkgs/main/win-64::pip-19.3.1-py37_0
  python             pkgs/main/win-64::python-3.7.5-h8c8aaf0_0
  setuptools         pkgs/main/win-64::setuptools-41.6.0-py37_0
  sqlite             pkgs/main/win-64::sqlite-3.30.1-he774522_0
  vc                 pkgs/main/win-64::vc-14.1-h0510ff6_4
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_0
  wheel              pkgs/main/win-64::wheel-0.33.6-py37_0
  wincertstore       pkgs/main/win-64::wincertstore-0.2-py37_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
setuptools-41.6.0    | 687 KB    | ####################################### | 100%
python-3.7.5         | 14.7 MB   | ####################################### | 100%
ca-certificates-2019 | 163 KB    | ####################################### | 100%
openssl-1.1.1d       | 5.7 MB    | ####################################### | 100%
sqlite-3.30.1        | 962 KB    | ####################################### | 100%
pip-19.3.1           | 1.9 MB    | ####################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cutadapt
#
# To deactivate an active environment, use
#
#     $ conda deactivate

and cutadapt was activated but commands are not working

[Mark]

FYI I am not the creator of this thread asking for help...

[ATpoint]

I know. Commenting on an existing chain keeps threads organized, it does not imply that I am specifically commenting on your comment.

[KD]

I have done this step, but yes I think I am making mistake at this point, but unable to figure it out

Answer 1

[ATpoint]

What you did was to create an environment called cutadapt but you did not install the tool itself. Activate this environment (or install into base, your preference) and type conda install -c bioconda cutadapt.

Edit: OP is using Windows, for which this solution is not appropriate, see comment below.

[KD]

Nopes.... not working

PackagesNotFoundError: The following packages are not available from current channels:

• cutadapt

Current channels:

• https://conda.anaconda.org/bioconda/win-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/win-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/win-64
• https://repo.anaconda.com/pkgs/r/noarch
• https://repo.anaconda.com/pkgs/msys2/win-64
• https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

[ATpoint]

You are using Windows, should have made that clear right away. Nothing wrong with Windows itself but typically bioinformatics is a Unix world and for cutadapt I do not think it is properly supported: https://github.com/marcelm/cutadapt/issues/315 Do yourself a favor and get a Linux partition, most bioinfo software runs on Unix, but not Windows.