Trouble shooting with cutadapt -bash: cutadapt: command not found

Question

[Pigasos83]

Hi all,

I recently installed the cutadapt with the: pip install --user --upgrade cut adapt I try to run the mode 3 of MaGeCK where I need to trim the 5'adapter seq for the fastq file ERR376998

The problem is that I do get the message: bash: cutadapt: command not found
,when I try to run the order : cutadapt -g CTTGTGGAAAGGACGAAACACCG -o output.fastq ERR376998.fastq

Any ideas why? Thank you very much!

Answer 1

[GenoMax]

What does which cutadapt produce? If it does not produce anything then the location where cutadapt was installed is not in your $PATH. You can find the directory where cutadapt is and add that to PATH by doing export PATH=/path_to_cutadapt_dir/:$PATH

[Pigasos83]

Dear genomax2, thanx much! But still the same problem

The which cutadapt does not produce anything. Entered export PATH=/path_to_cutadapt_dir/:$PATH and again had the same result: -bash: cutadapt: command not found

I type echo $PATH and the path was changed /path_to_cutadapt_dir/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

Any ideas?

[GenoMax]

Sorry if I was not clear. /path_to_cutadapt_dir needs to be replaced with a real directory on your machine.

Can you see if find ~ -name "cutadapt" produces a local directory listing (under your $HOME)? If that says /home/Pigasos83/.local/bin/cutadapt then (as an example) you would do export PATH=/home/Pigasos83/.local/bin/:$PATH

[Pigasos83]

thank you much! it worked :)

[GenoMax]

Perfect. Thanks for the confirmation.

[WouterDeCoster]

Good luck with the rest of your work. Please upvote the correct answer here to show your appreciation :-)

[Pigasos83]

Thanks for the heads up Wouter: Here I copy paste the correct commands: which cutadapt # to identify if the cutadapt is installed in your path. If it does not produce anything then the location where cutadapt was installed is not in your $PATH

find ~ -name "cutadapt" # produces a local directory listing (under your $HOME)?

export PATH=/home/Pigasos83/bin/:$PATH # exports the cutadapt on my $PATH

cutadapt -g CTTGTGGAAAGGACGAAACACCG -o output.fastq ERR376998.fastq # works!!!

Enjoy!