Hello. I’m running into a small problem when trying to use max-date in a special build. I’ve updated nextstrain to the most recent version, and the problem remains, so I don’t know what I’m doing wrong. My builds.yaml is set up like this:
subsampling: earlyG: focus: group_by: "year month" max_date: "2020-05-31" max_sequences: 1000 exclude: "--exclude-where 'Nextstrain_clade!=20G'" background: group_by: "year month" max_date: "2020-05-31" max_sequences: 100 exclude: "--exclude-where 'Nextstrain_clade!=20C'" priorities: type: "proximity" focus: "focus"
(I’m trying to look at the early cases of 20G, and the genetically closest known 20C cases in order to understand when and where the variant may have appeared)
When I try running this build, however, I get errors because the filter command is putting the ‘2020-05-31’ in the command line, but not the --max-date command before it:
Error in rule subsample: jobid: 23 output: results/earlyG/sample-focus.fasta, results/earlyG/sample-focus.txt log: logs/subsample_earlyG_focus.txt (check log file(s) for error message) shell: augur filter --sequences results/filtered_gisaid.fasta --metadata data/metadata_gisaid.tsv --sequence-index results/combined_sequence_index.tsv --include defaults/include.txt --exclude defaults/exclude.txt 2020-05-31 --exclude-where 'Nextstrain_clade!=20G' --group-by year month --subsample-max-sequences 1000 --output results/earlyG/sample-focus.fasta --output-strains results/earlyG/sample-focus.txt 2>&1 | tee logs/subsample_earlyG_focus.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Logfile logs/subsample_earlyG_focus.txt: ERROR: Could not open file of excluded strains '['defaults/exclude.txt', '2020-05-31']'
Because the --max-date is not in the command, it is treating the date in the command line as a modifier for the --exclude command.
What am I doing wrong? I’ve tried both max_date and max-date in the builds.yaml. Neither works. I have the same problem with min-date.