Hello,
I am using the nextstrain for the analysis of [SARS-CoV-2] sequencing data generated at our institute. I successfully, can execute the example file and getting the output in json format. However, when I run the nextsrtain on our SARS-CoV-2 data error popes up.
I am using default parameter.yaml file and my build.yaml is as follow :
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ACTREC_Maharashtra:
subsampling_scheme: division
region: Asia
country: India
division: Maharashtra
Error that popes up
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ERROR: All samples have been dropped! Check filter rules and metadata file format.
ERROR: All samples have been dropped! Check filter rules and metadata file format.
ERROR: All samples have been dropped! Check filter rules and metadata file format.
[Mon Sep 21 16:27:34 2020]
Error in rule subsample:
jobid: 21
output: results/ACTREC_Maharashtra/sample-country.fasta
shell:
augur filter --sequences results/masked.fasta --metadata /scratch/csllab/Nilesh/Softwares/ncov/our_info/metadata_updated.tsv --include defaults/include.txt --exclude-where 'region!=Asia' 'country!=India' 'division=Maharashtra' --priority results/ACTREC_Maharashtra/proximity_division.tsv --group-by division year month --sequences-per-group 20 --output results/ACTREC_Maharashtra/sample-country.fasta 2>&1 | tee
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)