augur refine is using TreeTime version 0.8.1
Traceback (most recent call last):
File “/home/mahan/miniconda3/envs/nextstrain/bin/augur”, line 10, in
sys.exit(main())
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/main.py”, line 10, in main
return augur.run( argv[1:] )
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/init.py”, line 75, in run
return args.command.run(args)
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/refine.py”, line 206, in run
tt = refine(tree=T, aln=aln, ref=ref, dates=dates, confidence=args.date_confidence,
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/refine.py”, line 36, in refine
tt = TreeTime(tree=tree, aln=aln, ref=ref, dates=dates,
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/treetime.py”, line 34, in init
super(TreeTime, self).init(*args, **kwargs)
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/clock_tree.py”, line 83, in init
self._assign_dates()
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/clock_tree.py”, line 130, in _assign_dates
raise MissingDataError(“ERROR: ALMOST NO VALID DATE CONSTRAINTS”)
treetime.MissingDataError: ERROR: ALMOST NO VALID DATE CONSTRAINTS
[Sat Apr 3 17:42:58 2021]
Error in rule refine:
jobid: 4
output: results/global/tree.nwk, results/global/branch_lengths.json
log: logs/refine_global.txt (check log file(s) for error message)
shell:
augur refine --tree results/global/tree_raw.nwk --alignment results/global/aligned.fasta --metadata data/1617434555337.metadata.tsv --output-tree results/global/tree.nwk --output-node-data results/global/branch_lengths.json --root Wuhan/Hu-1/2019 Wuhan/WH01/2019 --timetree --clock-rate 0.0008 --clock-std-dev 0.0004 --coalescent skyline --date-inference marginal --divergence-unit mutations --date-confidence --no-covariance --clock-filter-iqd 4 2>&1 | tee logs/refine_global.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/refine_global.txt:
augur refine is using TreeTime version 0.8.1
Traceback (most recent call last):
File “/home/mahan/miniconda3/envs/nextstrain/bin/augur”, line 10, in
sys.exit(main())
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/main.py”, line 10, in main
return augur.run( argv[1:] )
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/init.py”, line 75, in run
return args.command.run(args)
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/refine.py”, line 206, in run
tt = refine(tree=T, aln=aln, ref=ref, dates=dates, confidence=args.date_confidence,
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/augur/refine.py”, line 36, in refine
tt = TreeTime(tree=tree, aln=aln, ref=ref, dates=dates,
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/treetime.py”, line 34, in init
super(TreeTime, self).init(*args, **kwargs)
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/clock_tree.py”, line 83, in init
self._assign_dates()
File “/home/mahan/miniconda3/envs/nextstrain/lib/python3.9/site-packages/treetime/clock_tree.py”, line 130, in _assign_dates
raise MissingDataError(“ERROR: ALMOST NO VALID DATE CONSTRAINTS”)
treetime.MissingDataError: ERROR: ALMOST NO VALID DATE CONSTRAINTS
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/c/Users/Mahan/Desktop/ncov/.snakemake/log/2021-04-03T174249.033605.snakemake.log
please help me for this error