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Cutadapt error running trimgalore

Hello,

I am running into an issue when I run trimgalore that produces an error:

"Failed to execute Cutadapt porperly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt"

I have cutadapt sourced in the path so when I run $cutadapt --version from terminal it provides me with the correct version of 2.7. I have also tried modifying the --path_to_cutadapt option for trimgalore to specify where it is but I receive the same error message.

Has anyone else run into this issue and solved it?

Thanks!

trimgalore cutadapt software error sequencing
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written by mgdesaix • mgdesaix

1 answer

Solved. The issue was that I needed to edit the shebang in the cutadapt file because it was directing to a non-existent location for python. Since I had python loaded in the environment I just changed cutadapt to:

#! /usr/bin/env python from #!/usr/bin/python3

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written by mgdesaix • mgdesaix

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