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Troubleshooting

Jill V. Hagey, PhD edited this page Aug 2, 2022 · 9 revisions

Once version 1.0 of the pipeline is released after beta-testing this page will contain examples of what we consider good/bad genome assemblies and our reasoning for it.

Errors

If you run:

nextflow run cdcgov/phoenix -profile singularity,test -entry PHOENIX --kraken2db $PWD/Kraken2DB/

You might run into an error that says something like:

N E X T F L O W ~ version 21.10.6
Project `cdcgov/phoenix` currently is sticked on revision: v1.0.0 -- you need to specify explicitly a revision with the option `-r` to use it

This is because you need to tell nextflow what version (tag/branch) of the PHoeNIx you want to run by using the -r option. For more information see the nf-core documentation

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