Hi all
got this error trying to install the test data. any advice?
Thanks, ibz
(nextstrain) ibz@C02DW5NDMD6T ncov % snakemake --cores 4 --profile ./my_profiles/getting_started
localrules directive specifies rules that are not present in the Snakefile:
upload
Building DAG of jobs…
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job counts:
count jobs
1 align
1 all
1 ancestral
1 clades
1 combine_samples
1 diagnostic
1 export
1 filter
1 finalize
1 incorporate_travel_history
1 mask
1 recency
1 refilter
1 refine
1 rename_subclades
1 subclades
1 subsample
1 tip_frequencies
1 traits
1 translate
1 tree
21
[Tue Jan 26 12:53:31 2021]
Job 22:
Aligning sequences to defaults/reference_seq.fasta
- gaps relative to reference are considered real
mafft --auto --thread 4 --keeplength --addfragments results/prefiltered.fasta defaults/reference_seq.fasta > results/aligned.fasta 2> logs/align.txt
[Tue Jan 26 12:53:44 2021]
Finished job 22.
1 of 21 steps (5%) done
[Tue Jan 26 12:53:44 2021]
Job 23: Scanning aligned sequences results/aligned.fasta for problematic sequences
python3 scripts/diagnostic.py --alignment results/aligned.fasta --metadata data/example_metadata.tsv --reference defaults/reference_seq.gb --mask-from-beginning 100 --mask-from-end 50 --output-flagged results/flagged-sequences.tsv --output-diagnostics results/sequence-diagnostics.tsv --output-exclusion-list results/to-exclude.txt 2>&1 | tee logs/diagnostics.txt
[Tue Jan 26 12:53:44 2021]
Job 12: Use metadata on submission date to construct submission recency field
python3 scripts/construct-recency-from-submission-date.py --metadata data/example_metadata.tsv --output results/global/recency.json 2>&1 | tee logs/recency_global.txt
Traceback (most recent call last):
File “scripts/construct-recency-from-submission-date.py”, line 3, in
from augur.utils import read_metadata
ModuleNotFoundError: No module named ‘augur’
[Tue Jan 26 12:53:44 2021]
Error in rule recency:
jobid: 12
output: results/global/recency.json
log: logs/recency_global.txt (check log file(s) for error message)
shell:
python3 scripts/construct-recency-from-submission-date.py --metadata data/example_metadata.tsv --output results/global/recency.json 2>&1 | tee logs/recency_global.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/recency_global.txt:
Traceback (most recent call last):
File “scripts/construct-recency-from-submission-date.py”, line 3, in
from augur.utils import read_metadata
ModuleNotFoundError: No module named ‘augur’
Traceback (most recent call last):
File “scripts/diagnostic.py”, line 8, in
from Bio.SeqIO.FastaIO import SimpleFastaParser
ModuleNotFoundError: No module named ‘Bio’
[Tue Jan 26 12:53:44 2021]
Error in rule diagnostic:
jobid: 23
output: results/sequence-diagnostics.tsv, results/flagged-sequences.tsv, results/to-exclude.txt
log: logs/diagnostics.txt (check log file(s) for error message)
shell:
python3 scripts/diagnostic.py --alignment results/aligned.fasta --metadata data/example_metadata.tsv --reference defaults/reference_seq.gb --mask-from-beginning 100 --mask-from-end 50 --output-flagged results/flagged-sequences.tsv --output-diagnostics results/sequence-diagnostics.tsv --output-exclusion-list results/to-exclude.txt 2>&1 | tee logs/diagnostics.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/diagnostics.txt:
Traceback (most recent call last):
File “scripts/diagnostic.py”, line 8, in
from Bio.SeqIO.FastaIO import SimpleFastaParser
ModuleNotFoundError: No module named ‘Bio’
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /Users/ibz/ncov/.snakemake/log/2021-01-26T125331.400352.snakemake.log
(nextstrain) ibz@C02DW5NDMD6T ncov %