Marcel Martin

I think you can get what you want by using `-a CATGN{20}X`, that is, a [non-internal 3' adapter](https://cutadapt.readthedocs.io/en/latest/guide.html#non-internal). You can see the `X` as not being allowed to match any...

You’re right, `--action=retain` won’t work the way you need it. I don’t think the linked adapters approach works either. I don’t have any further suggestions at the moment except that...

Some notes. To me, the biggest problem for things like this is how to design the user interface. A couple of ideas: 1. Use sth. like `--order=trim,cut,qtrim,rename` 2. Add an...

I’ll have a look after my vacation.

You you please add the `--debug` option and paste the log output here?

A couple of further thoughts. - I noticed that you added `;min_overlap=24` to all adapters in the `adaptersLeft.fa` file. If the minimum overlap is identical for all adapters anyway, you...

Thanks, looking at the debug log, I see that many `pigz` processes are started to handle compression, which is perhaps the problem. Since you write to 182 * 2 =...

Alright! It’s a bit weird because both log outputs you sent me indicate that the program is actually doing something, so it should at least have some CPU usage and...

I think I was now able to reproduce this locally. Perhaps I can find a way to fix this. Thanks for reporting.

I’ll need to re-open this so I don’t forget.