I updated Nextstrain-cli from 3.0.3. to nextstrain-cli, 3.0.6 by running nextstrain update , Then python3.8 -m pip install --upgrade nextstrain-cli. Afterthat, I ran the script again.
The first error message is gone, but the second still appearing:
Error in rule sanitize_metadata:
jobid: 26
output: results/sanitized_metadata_RUNTEST.tsv.xz
log: logs/sanitize_metadata_RUNTEST.txt (check log file(s) for error message)
shell:
python3 scripts/sanitize_metadata.py --metadata data/RUNTEST.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_RUNTEST.tsv.xz 2>&1 | tee logs/sanitize_metadata_RUNTEST.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/sanitize_metadata_RUNTEST.txt:
Traceback (most recent call last):
File "/mnt/e/Bioinformatics/nextstrain/nextstrain/ncov/scripts/sanitize_metadata.py", line 2, in <module>
from augur.io import open_file, read_metadata
ModuleNotFoundError: No module named 'augur'
I have checked the issue here and this is the output of which python3
/home/linuxbrew/.linuxbrew/bin/python3
any ideas on how to solve it?
Thank you