cutadapt | Cutadapt removes adapter sequences from sequencing reads | Genomics library

Try to locate from which path cutadapt is executed with this command in powershell where cutadapt, there is probably 2 versions of your package (one from python2 for example)

You can also run this python3 -m cutadapt --version, that should run the latest version.

Snakemake uses the Python formatting, so you can escape curly brace with another curly brace:

Turns out, that I had some problems with python 3.5, so I switched to python 3.8 and managed to install the package.

What in many languages are known as "heredocs" are typically called "triple-quoted strings" in Python. You simply need to create a triple-quoted f-string:

I could not reproduce your issue with a recent cutadapt version (cutadapt 2.5 with Python 3.7.3), installed using conda (cutadapt-2.5 package from bioconda channel). All 5 commands succeeded, giving the expected output (either 1 or 2 reads are trimmed, either 1 or 2 reads are written in the output). I used bash and zsh shells and perl v5.18.2 without an issue. According to your output, you are using an older cutadapt version (cutadapt 1.18 with Python 3.7.1.).

Try installing a recent cutadapt version using conda, see directions below. This is the most likely cause of your issue.

Installing cutadapt using conda (assuming conda is already installed and bioconda is included in the channels):

Instead of trying to do this with %s placeholders, I would try .format(), like so:

You need to separate all the arguments; "--cut 20" passes a single argument containing both the switch and its value (that it, it tells program it received a single switch named cut 20). You'd only pass it as a single argument if, at the command line, you literally passed "--cut 20" in quotes to prevent the whitespace from breaking it up into separate pieces of the program's argv (which you clearly don't in your example).

Split it up to "--cut", "20" and it should work.

There is no way to ensure this via snakemake. However the problem does not occur at all if you use the logging support of snakemake itself, which has the additional benefit of being independent of the execution platform: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

In that case, directories will of course be created by snakemake of they are not already present. Moreover, error messages will directly point you to the right log file.

Check carefully the cutadapt documentation, there's a specific chapter regarding paired end alignments. You are looking for -A.

You are also messing things up with the --interleaved parameter: if the reads are interleaved, why are you giving the two ends? I'm not sure what are you trying to achieve, but I bet you have an extra cutadapt invocation.

I guess you are trying something like: