split_on_adapter: Missing internal adapter/primer from the middle of the main read

[Gazal90]

Hi,

I am trying to use the "split_on_adapter" functionality to split chimeric ONT reads into sub-reads.

Since we are using different adapters and primers than the one specified in the script, I edited them in the script.

The script seems to be running fine, splitting the reads into sub-reads. But the adapter matches in the middle of the main read are skipped in the output split.fastq file.

To explain better the output sub-read headers are as follows: The first sub-read: x_1 None 0->563 The second sub-read: x_2 None 672->1511

The bases from 564 to 671 are absent from the output file.

Maybe I'm doing something wrong? Because the manual specifies that the output would be just splitting the reads; not removing anything.