Frequently Asked Questions

Genomepy utilizes external databases to obtain your files. Unfortunately this sometimes causes issues. Here are some of the more common issues, with solutions.

Let us know if you encounter issues you cannot solve by creating a new issue.

Provider is offline

Occasionally one of the providers experience connection issues, which can last anywhere between minutes to hours. When this happens genomepy will warn that the provider appears offline, or that the URL seems broken.

If the issue does not pass, you can try to reset genomepy. Simply run genomepy clean on the command line, or run genomepy.clean() in Python.

This genome is missing

Genomepy stores provider data on your computer to rerun it faster later. If a provider was offline during this time, it may miss (parts of) the data.

To re-download the data, remove the local data with genomepy clean, then search for your genome again.

This genome is STILL missing/URL is broken

Sadly, not everything (naming, structure, filenames) is always consistent on the provider end. Contact the provider to get it fixed! One notable group are Ensembl fungi, which seems to be mostly mislabelled.

In the meantime, you can still use the power of genomepy by manually retrieving the URLs, and downloading the files with genomepy install GENOME_URL -p url --url-to-annotation ANNOTATION_URL.

The genomepy config was corrupted

You can create a new one with genomepy config generate on command line, or genomepy.manage_config("generate") in Python.

What’s genomepy maximum memory usage?

Genomepy does not read a genome fully into memory. Therefore, installing takes less than 1 GB RAM regardless of the genome’s size. Searching NCBI is the most costly operation, using around 3 GB (the first time).

Which genome/gene annotation to use

Each provider has its pros and cons:

  • Ensembl has excellent gene annotations, but their chromosome names can cause issues with some tools.

  • UCSC has an excellent genome browser, but their gene annotations vary in format.

  • NCBI allows public submissions, and so has the latest versions, although not always complete or error free.

Use genomepy search to see your options, and genomepy annotation to check the quality of the gene annotation(s).