kfuku52 / csubst

Molecular convergence detection

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ValueError:Quantiles #52

Closed agneeshbarua closed 9 months ago

agneeshbarua commented 9 months ago

Dear Kenji,

I am running CSUSBT and have encountered the following error:

File "<__array_function__ internals>", line 200, in quantile File "/users/abarua/myproject_envs/Pigmentation_env/lib/python3.11/site-packages/numpy/lib/function_base.py", line 4460, in quantile raise ValueError("Quantiles must be in the range [0, 1]")

I've attached a folder containing all the data that gave me this error. value_test.zip

kfuku52 commented 9 months ago

Thank you for reporting! Could you share the CSUBST command you used?

kfuku52 commented 9 months ago

I got different error. Is it the tree you used as a CSUBST input?

ValueError: Internal node labels are not unique. Please provide unique internal node labels or delete them from --rooted_tree_file. For the label deletion, nwkit drop may be useful: https://github.com/kfuku52/nwkit/wiki/nwkit-drop

agneeshbarua commented 9 months ago

Here is the command:

Run CSUBST

csubst analyze --alignment_file ../$name"_cds_hammer.fa" \ --rooted_tree_file ../$name"_generax.nwk" \ --threads 4 \ --cutoff_stat 'OCNany2spe,3.0|omegaCany2spe,5.0' \ --max_arity 10

$name = Orthogroup name (OG)

Not sure why you got the node label error, the files have the same sets of genes.

kfuku52 commented 9 months ago

OK, I will delete internal node names.

kfuku52 commented 9 months ago

The bug should be fixed now. Please feel free to reopen the issue if the problem persists.