Thank you Martin, I will first try to install the latest release (0.20.1) to create a fresh environment and then see if it will solve the issue. If not, I will try again when the next release is out for passing accelerator into Trainer!
Another question, I tried running the training and subsequent steps without GPU and it went great. However, I got stuck at the Differential gene expression step and here is the error. I am hoping you could possibly help me identify how to modify my adata to make it work since it went fine with the tutorial PBMC dataset.
I already filtered the adata so that protein and RNA share the same cells. The full traceback are below. Somehow the index of the adata is messed up and is throwing the error?
DE…: 0%| | 0/18 [00:39<?, ?it/s]
KeyError Traceback (most recent call last)
Cell In [25], line 1
----> 1 de_df = vae.differential_expression(groupby = “cell_calls”)
2 de_df.head(5)
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/scvi/model/_totalvi.py:763, in TOTALVI.differential_expression(self, adata, groupby, group1, group2, idx1, idx2, mode, delta, batch_size, all_stats, batch_correction, batchid1, batchid2, fdr_target, silent, protein_prior_count, scale_protein, sample_protein_mixing, include_protein_background, **kwargs)
749 model_fn = partial(
750 self._expression_for_de,
751 scale_protein=scale_protein,
(…)
755 batch_size=batch_size,
756 )
757 col_names = np.concatenate(
758 [
759 np.asarray(_get_var_names_from_manager(adata_manager)),
760 self.protein_state_registry.column_names,
761 ]
762 )
→ 763 result = _de_core(
764 adata_manager,
765 model_fn,
766 groupby,
767 group1,
768 group2,
769 idx1,
770 idx2,
771 all_stats,
772 cite_seq_raw_counts_properties,
773 col_names,
774 mode,
775 batchid1,
776 batchid2,
777 delta,
778 batch_correction,
779 fdr_target,
780 silent,
781 **kwargs,
782 )
784 return result
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/scvi/model/base/_utils.py:267, in de_core(adata_manager, model_fn, groupby, group1, group2, idx1, idx2, all_stats, all_stats_fn, col_names, mode, batchid1, batchid2, delta, batch_correction, fdr, silent, **kwargs)
265 res = res.sort_values(by=sort_key, ascending=False)
266 if mode == “change”:
→ 267 res[f"is_de_fdr{fdr}"] = _fdr_de_prediction(res[“proba_de”], fdr=fdr)
268 if idx1 is None:
269 g2 = “Rest” if group2 is None else group2
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/scvi/model/base/_utils.py:288, in _fdr_de_prediction(posterior_probas, fdr)
286 raise ValueError(“posterior_probas should be 1-dimensional”)
287 sorted_genes = np.argsort(-posterior_probas)
→ 288 sorted_pgs = posterior_probas[sorted_genes]
289 cumulative_fdr = (1.0 - sorted_pgs).cumsum() / (1.0 + np.arange(len(sorted_pgs)))
290 d = (cumulative_fdr <= fdr).sum()
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/series.py:984, in Series.getitem(self, key)
981 key = np.asarray(key, dtype=bool)
982 return self._get_values(key)
→ 984 return self._get_with(key)
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/series.py:1019, in Series._get_with(self, key)
1015 if key_type == “integer”:
1016 # We need to decide whether to treat this as a positional indexer
1017 # (i.e. self.iloc) or label-based (i.e. self.loc)
1018 if not self.index._should_fallback_to_positional:
→ 1019 return self.loc[key]
1020 else:
1021 return self.iloc[key]
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexing.py:967, in _LocationIndexer.getitem(self, key)
964 axis = self.axis or 0
966 maybe_callable = com.apply_if_callable(key, self.obj)
→ 967 return self._getitem_axis(maybe_callable, axis=axis)
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexing.py:1194, in _LocIndexer._getitem_axis(self, key, axis)
1191 if hasattr(key, “ndim”) and key.ndim > 1:
1192 raise ValueError(“Cannot index with multidimensional key”)
→ 1194 return self._getitem_iterable(key, axis=axis)
1196 # nested tuple slicing
1197 if is_nested_tuple(key, labels):
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexing.py:1132, in _LocIndexer._getitem_iterable(self, key, axis)
1129 self._validate_key(key, axis)
1131 # A collection of keys
→ 1132 keyarr, indexer = self._get_listlike_indexer(key, axis)
1133 return self.obj._reindex_with_indexers(
1134 {axis: [keyarr, indexer]}, copy=True, allow_dups=True
1135 )
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexing.py:1330, in _LocIndexer._get_listlike_indexer(self, key, axis)
1327 ax = self.obj._get_axis(axis)
1328 axis_name = self.obj._get_axis_name(axis)
→ 1330 keyarr, indexer = ax._get_indexer_strict(key, axis_name)
1332 return keyarr, indexer
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexes/base.py:5796, in Index._get_indexer_strict(self, key, axis_name)
5793 else:
5794 keyarr, indexer, new_indexer = self._reindex_non_unique(keyarr)
→ 5796 self._raise_if_missing(keyarr, indexer, axis_name)
5798 keyarr = self.take(indexer)
5799 if isinstance(key, Index):
5800 # GH 42790 - Preserve name from an Index
File ~/miniconda3/envs/scanpy_env/lib/python3.10/site-packages/pandas/core/indexes/base.py:5859, in Index._raise_if_missing(self, key, indexer, axis_name)
5856 raise KeyError(f"None of [{key}] are in the [{axis_name}]“)
5858 not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique())
→ 5859 raise KeyError(f”{not_found} not in index")
KeyError: ‘[239, 238, 237, 235, 234, 233, 236, 231, 230, 229, 232, 245, 244, 243, 241, 240, 242, 255, 260, 259, 258, 257, 256, 254, 248, 252, 251, 250, 249, 253, 247, 246, 274, 273, 272, 271, 270, 269, 268, 266, 265, 264, 263, 262, 261, 267, 286, 293, 292, 291, 290, 289, 288, 287, 285, 284, 283, 282, 281, 280, 279, 278, 277, 276, 275, 307, 306, 305, 304, 303, 302, 301, 299, 298, 297, 296, 295, 294, 300, 317, 322, 321, 320, 319, 318, 315, 316, 314, 313, 312, 311, 310, 309, 308, 337, 336, 335, 334, 333, 332, 330, 331, 328, 327, 326, 325, 324, 323, 329, 348, 349, 350, 351, 355, 353, 354, 356, 352, 347, 344, 345, 343, 342, 341, 340, 339, 338, 346, 370, 369, 368, 367, 366, 365, 364, 361, 362, 360, 359, 358, 357, 363, 384, 383, 389, 382, 386, 387, 388, 385, 381, 375, 379, 378, 377, 376, 374, 373, 372, 371, 380, 405, 406, 407, 408, 413, 410, 411, 412, 404, 409, 402, 403, 400, 401, 390, 391, 392, 394, 393, 396, 397, 398, 399, 395, 433, 430, 431, 432, 434, 440, 436, 437, 438, 441, 429, 435, 428, 439, 426, 427, 414, 416, 417, 418, 419, 415, 421, 422, 423, 424, 425, 420, 453, 461, 460, 459, 458, 457, 456, 455, 454, 452, 462, 450, 449, 448, 447, 446, 445, 444, 443, 442, 451, 474, 476, 477, 481, 479, 480, 473, 478, 472, 475, 470, 469, 468, 467, 466, 465, 464, 463, 471, 500, 501, 502, 503, 504, 505, 506, 511, 508, 509, 512, 513, 514, 499, 507, 498, 510, 496, 482, 483, 485, 497, 486, 487, 488, 484, 490, 491, 492, 493, 494, 495, 489, 529, 530, 531, 532, 536, 534, 535, 537, 528, 533, 527, 525, 517, 524, 523, 522, 521, 520, 519, 518, 516, 515, 526, 556, 555, 553, 557, 554, 558, 564, 560, 561, 562, 563, 565, 559, 552, 538, 550, 551, 539, 540, 541, 543, 542, 545, 546, 547, 548, 549, 544, 584, … 32071, 32072, 32073, 32074, 32075, 32076, 32077, 32078, 32079, 32080, 32081, 32082, 32083, 32084, 32085, 32086, 32087, 32088, 32089, 32090, 32091, 32092, 32093, 32094, 32095, 32096, 32097, 32098, 32099, 32100, 32101, 32102, 32103, 32104, 32105, 32106, 32107, 32108, 32109, 32110, 32111, 32112, 32113, 32114, 32115, 32116, 32117, 32118, 32119, 32120, 32121, 32122, 32123, 32124, 32125, 32126, 32127, 32128, 32129, 32130, 32131, 32132, 32133, 32134, 32135, 32136, 32137, 32138, 32139, 32140, 32141, 32142, 32143] not in index’
