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skyline: TypeError: can't multiply sequence by non-int of type 'float' #256

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judyssister opened this issue Aug 17, 2023 · 0 comments
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@judyssister
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Dear authors,

Thanks a lot for providing the wonderful tools.
I am faced with an error when I run:
treetime --tree RAxML_bipartitions_ha_v3 --dates treetime_ha.csv --aln ha_v3_trim.fasta --time-marginal true --coalescent skyline --n-skyline 50 --outdir 01_timetree

Inferred coalescent model
Traceback (most recent call last):
File "/Users/yangjing/Library/Python/3.7/bin/treetime", line 8, in
sys.exit(main())
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/main.py", line 21, in main
return_code = params.func(params)
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/argument_parser.py", line 233, in toplevel
timetree(params)
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/wrappers.py", line 332, in timetree
return run_timetree(myTree, params, outdir)
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/wrappers.py", line 446, in run_timetree
print_save_plot_skyline(myTree, plot=basename+'skyline.pdf', save=basename+'skyline.tsv', screen=True, gen=params.gen_per_year)
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/CLI_io.py", line 204, in print_save_plot_skyline
skyline, conf = tt.merger_model.skyline_inferred(gen=gen, confidence=n_std)
File "/Users/yangjing/Library/Python/3.7/lib/python/site-packages/treetime/merger_models.py", line 387, in skyline_inferred
conf = [skyline.ynp.exp(-confidenceself.confidence), skyline.ynp.exp(confidenceself.confidence)]
TypeError: can't multiply sequence by non-int of type 'float'

However, it does work and no error is reported if I run the following:
treetime --tree RAxML_bipartitions_ha_v3 --dates treetime_ha.csv --aln ha_v3_trim.fasta --time-marginal true --outdir 01_timetree

Could you please let me know where I am wrong?

Thank you very much.
Jing

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