The

Process exceeded running time limit (16h)

is probably key. Try extending the time limit for Eukulele with a config file similar to the below:

process {
    withName: EUKULELE_SEARCH {
        time = 48.h
    }
}

You can pass config files in different ways: https://nf-co.re/docs/running/configuration/configuration-options#custom-configuration-files I always just create a

nextflow.config

file in the directory from which I run Nextflow.