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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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Error when trying to run magic #44

Closed kbrulois closed 6 years ago

kbrulois commented 7 years ago

I'm having trouble getting MAGIC.py to run. Tried the gui and command line. I'm using macOS 10.12.5 Python stops responding and it gives this error message:

(python3) SLE-BTR-C02TN2K4HF1R:magic kevin$ MAGIC.py -d /Users/kevin/Desktop/test.csv -o /Users/kevin/Desktop/ csv ^CTraceback (most recent call last): File "/usr/local/bin/MAGIC.py", line 112, in main(sys.argv[1:]) File "/usr/local/bin/MAGIC.py", line 95, in main scdata.filter_scseq_data(filter_cell_min=args.mols_per_cell_min, filter_cell_max=args.mols_per_cell_max) File "/usr/local/lib/python3.6/site-packages/magic/mg.py", line 476, in filter_scseq_data self.data = self.data.ix[self.data.index[to_keep], :].astype(np.float32) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 118, in getitem return self._getitem_tuple(key) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 856, in _getitem_tuple retval = getattr(retval, self.name)._getitem_axis(key, axis=i) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1059, in _getitem_axis return self._getitem_iterable(key, axis=axis) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1118, in _getitem_iterable keyarr) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2916, in _reindex_non_unique indexer, missing = self.get_indexer_non_unique(target) File "/usr/local/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2708, in get_indexer_non_unique indexer, missing = self._engine.get_indexer_non_unique(tgt_values) File "pandas/_libs/index.pyx", line 356, in pandas._libs.index.IndexEngine.get_indexer_non_unique (pandas/_libs/index.c:8161) File "/usr/local/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 1136, in resize a = concatenate((a,)*n_copies) KeyboardInterrupt

pkathail commented 7 years ago

Could you post the full stack trace of the error or is it too long? With the keyboard interrupt it's difficult to determine the reason for the error

danieldager commented 6 years ago

Hi kbrulois,

There's a good chance that these problems were resolved with the release of MAGIC v1.0. Uninstall your current version of MAGIC and reinstall per the directions of the new README. I'm closing this for now; please feel free to open a new issue if you still have problems!