Troubleshooting and FAQs

I get a warning during CENTRIFUGE_KREPORT or KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE process with exit status 255

When a sample has insufficient hits for abundance estimation, the resulting report.txt file will be empty.

When trying to convert this to a kraken-style report or merging together, the tools will exit with a status code 255, and provide a WARN.

This is not an error nor a failure of the pipeline, just your sample has no hits to the provided database when using Centrifuge.

Why does any error or failed process from BRACKEN_BRACKEN get ignored?

If Kraken2 doesn’t classify any reads (100% unclassified) Bracken will fail on that input. Having no reads taxonomically classified can be a reasonable outcome for some samples, and we don’t want to treat this as an error.

Therefore to allow the remainder of a given run to complete if a single Bracken task fails, we set the Nextflow errorStrategy to ignore. You will still get a warning in the Nextflow console output and log that a Bracken task failed.

If you want to change this behaviour, you can override the errorStrategy in your own Nextflow configuration file.

For example:

process {
    withName: BRACKEN_BRACKEN {
        errorStrategy = 'retry'
    }
}

Other errorStrategy options can be found on the Nextflow documentation.