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Troubleshooting

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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

DISCLAIMER: The identification methods used and the data summarized are for public health surveillance or investigational purposes only and must NOT be communicated to the patient, their care provider, or placed in the patient’s medical record. These results should NOT be used for diagnosis, treatment, or assessment of individual patient health or management.

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