Question: Trouble shooting with cutadapt -bash: cutadapt: command not found
0
gravatar for Pigasos83
2.1 years ago by
Pigasos830
USA/NCI
Pigasos830 wrote:

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!

cutadapt sgrna seq • 1.8k views
ADD COMMENTlink written 2.1 years ago by Pigasos830

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax51k

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?

ADD REPLYlink written 2.1 years ago by Pigasos830

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax51k

thank you much! it worked :)

ADD REPLYlink written 2.1 years ago by Pigasos830

Perfect. Thanks for the confirmation.

ADD REPLYlink written 2.1 years ago by genomax51k

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

ADD REPLYlink written 2.1 years ago by WouterDeCoster30k

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!

ADD REPLYlink written 2.1 years ago by Pigasos830
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