I’m running Nextstrain with three builds (division, country, and global). Division and country seem to run fine but I ran into the following error message with the country build:
Error in rule proximity_score:
log: logs/subsampling_priorities_Australia_country.txt (check log file(s) for error message)
/home/minion/opt/miniconda3/envs/nextstrain/bin/python scripts/priorities.py --alignment results/masked.fasta --metadata data/global_metadata.tsv --reference defaults/reference_seq.gb --focal-alignment results/Australia/sample-country.fasta --output results/Australia/proximity_country.tsv 2>&1 | tee logs/subsampling_priorities_Australia_country.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
If I then restart the analysis without the country build, it seems to run fine.
I’m ok with just the division build I think but just curious as to why there’s an error in the country build only given it’s using the same data and scripts.