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Troubleshooting
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.
First make sure your Nextflow >=21.10.6 and Singularity >=3.8.0 are up-to-date, we have seen errors with older version of both software.
If you run PHoeNix with nextflow run cdcgov/phoenix ... you may encounter this error:
N E X T F L O W ~ version 21.10.6
Project `cdcgov/phoenix` contains uncommitted changes -- Cannot switch to revision: v1.0.0
This happens when the pipeline was not allowed to run to completion and files were changed without the pipeline getting to the steps to reset them for the next run. To reset the pipeline run the following:
gzip ~/.nextflow/assets/cdcgov/phoenix/assets/databases/REFSEQ_20210820_Bacteria_complete.msh
rm -f ~/.nextflow/assets/cdcgov/phoenix/assets/databases/Ref_Seq/*.gzIf you run:
nextflow run cdcgov/phoenix -profile singularity,test -entry PHOENIX --kraken2db $PATH_TO_DBYou 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 itThis is because you need to tell nextflow what version (tag/branch) of the PHoeNIx you want to run by using the -r option. So instead run:
nextflow run cdcgov/phoenix -r v1.0.0 -profile singularity,test -entry PHOENIX --kraken2db $PATH_TO_DBFor 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.