Hi @AroobAlhumaidy, I’m not sure if this is the same issue described in this other post, since the log file itself isn’t getting created.
What happens when you run the sanitize metadata command by itself like so from your nextstrain Conda environment?
python3 scripts/sanitize_metadata.py \
--metadata data/references_metadata.tsv \
--metadata-id-columns strain name 'Virus name' \
--database-id-columns 'Accession ID' gisaid_epi_isl genbank_accession \
--parse-location-field Location \
--rename-fields 'Virus name=strain' Type=type 'Accession ID=gisaid_epi_isl' 'Collection date=date' 'Additional location information=additional_location_information' 'Sequence length=length' Host=host 'Patient age=patient_age' Gender=sex Clade=GISAID_clade 'Pango lineage=pango_lineage' pangolin_lineage=pango_lineage Lineage=pango_lineage 'Pangolin version=pangolin_version' Variant=variant 'AA Substitutions=aa_substitutions' aaSubstitutions=aa_substitutions 'Submission date=date_submitted' 'Is reference?=is_reference' 'Is complete?=is_complete' 'Is high coverage?=is_high_coverage' 'Is low coverage?=is_low_coverage' N-Content=n_content GC-Content=gc_content \
--strip-prefixes hCoV-19/ SARS-CoV-2/ \
--output results/sanitized_metadata_refrences.tsv.xz 2>&1 | tee logs/sanitize_metadata_refrences.txt
My first thought is that the tee command does not exist or is not behaving like we’d expect.