Some African Countries (Burkina Faso, Sierra Leone) Build failed

[AlbertRockG]

Current Behavior

I would like to run a build for some specific African countries. So I firstly try to run your builds before modifying the YAML file. Because interested in CAMES (African and Malagasy Council for Higher Education), I checked out the build of countries belonging to this organisation, but some are actually missing. I have also check out the build of western africa and noticed that auspice was not able to select those countries (Burkina Faso and Sierra Leone for instance). This behaviour was noticed on the local run and also on nextstrain.org.

How to reproduce

Steps to reproduce the current behavior.

Your environment: if browsing Nextstrain online

• Operating system: Ubuntu 20.04 LTS
• Browser: firefox

Your environment: if running Nextstrain locally

• Operating system: Ubuntu 20.04 LTS
• Browser: firefox
• Version: auspice 2.41

[j23414]

Hi @AlbertRockG! We just merged https://github.com/nextstrain/ncov/pull/988 which should fix this issue. Thanks for reaching out!

Should be able to pull a new ncov and run a test for Burkina Faso using:

nextstrain build \
  --cpus 4 \
  --memory 8Gib \
  . \
  --configfile ../ncov-africa-cdc/builds_africa.yaml \
  --config active_builds=burkina-faso

But please let us know if the issue persists.

[AlbertRockG]

Sorry, I just try it and the issue persists.

[j23414]

Hi @AlbertRockG any interest in jumping on a zoom call? That way I can take a look?

My initial impression is you may need to pull the new ncov or delete a cached run (remove .snakemake and several intermediate files from data). It might be easiest to run the instructions in a new folder.

But it's easier to debug on a call since computer systems can be different.

[AlbertRockG]

Sure! You're right, it's easier. Can we do it now, please?

[j23414]

@AlbertRockG Sure! Please join [deleted link] I'll delete this link later.

Can send a screenshot when run completes, thanks!

[AlbertRockG]

@j23414 Thanks a lot, it worked!