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caporaso-lab / sourcetracker2

SourceTracker2
BSD 3-Clause "New" or "Revised" License
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Error when trying to run ST2. #94

Closed mawij2002 closed 5 years ago

mawij2002 commented 6 years ago

Hi,

The previous version (installed as indicated in the README) worked but it did not have the per_feature_assignment option. I have installed the most recent (as indicated in another issue thread (https://github.com/biota/sourcetracker2/issues/85). The thing is that with the new one install I cannot make it work. It gives me an error (copied below). Can you guys help me out? Thanks!

JP.

/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters Traceback (most recent call last): File "/Users/jm44736-mac/miniconda2/envs/st2/bin/sourcetracker2", line 11, in load_entry_point('sourcetracker==2.0.1.dev0', 'console_scripts', 'sourcetracker2')() File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/click/core.py", line 722, in call return self.main(args, kwargs) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/click/core.py", line 535, in invoke return callback(args, **kwargs) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/sourcetracker/_cli/gibbs.py", line 161, in gibbs_cli intersect_and_sort_samples(sample_metadata, feature_table) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/sourcetracker/_sourcetracker.py", line 127, in intersect_and_sort_samples shared_samples = np.intersect1d(sample_metadata.index, feature_table.index) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/numpy/lib/arraysetops.py", line 334, in intersect1d ar1 = unique(ar1) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/numpy/lib/arraysetops.py", line 210, in unique return _unique1d(ar, return_index, return_inverse, return_counts) File "/Users/jm44736-mac/miniconda2/envs/st2/lib/python3.5/site-packages/numpy/lib/arraysetops.py", line 277, in _unique1d ar.sort() TypeError: unorderable types: float() < str()

@gregcaporaso @wdwvt1

lkursell commented 6 years ago

Hi @mawij2002 - that TypeError suggests that we should check the formatting of your input files. Can you check that the values in the OTU table are stored as integers, and not as strings?