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scanpy sc.pp.calculate_qc_metrics(adata, qc_vars=["mt"], inplace=True)
See original GitHub issueAfter I use function
adata = sc.read_visium(
'./', count_file='V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5',
genome=None, library_id=None, load_images=True,
)
I use sc.pp.calculate_qc_metrics(adata, qc_vars=["mt"], inplace=True) and got an error message:
RuntimeError Traceback (most recent call last)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\errors.py in new_error_context(fmt_, *args, **kwargs)
744 try:
--> 745 yield
746 except NumbaError as e:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower_block(self, block)
272 loc=self.loc, errcls_=defaulterrcls):
--> 273 self.lower_inst(inst)
274 self.post_block(block)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower_inst(self, inst)
485 if isinstance(inst, _class):
--> 486 func(self, inst)
487 return
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\parfors\parfor_lowering.py in _lower_parfor_parallel(lowerer, parfor)
239 lowerer, parfor, typemap, typingctx, targetctx, flags, {},
--> 240 bool(alias_map), index_var_typ, parfor.races)
241 finally:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\parfors\parfor_lowering.py in _create_gufunc_for_parfor_body(lowerer, parfor, typemap, typingctx, targetctx, flags, locals, has_aliases, index_var_typ, races)
1326 flags,
-> 1327 locals)
1328
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in compile_ir(typingctx, targetctx, func_ir, args, return_type, flags, locals, lifted, lifted_from, is_lifted_loop, library, pipeline_class)
666 return pipeline.compile_ir(func_ir=func_ir, lifted=lifted,
--> 667 lifted_from=lifted_from)
668
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in compile_ir(self, func_ir, lifted, lifted_from)
348 FixupArgs().run_pass(self.state)
--> 349 return self._compile_ir()
350
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_ir(self)
407 assert self.state.func_ir is not None
--> 408 return self._compile_core()
409
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_core(self)
380 if is_final_pipeline:
--> 381 raise e
382 else:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_core(self)
371 try:
--> 372 pm.run(self.state)
373 if self.state.cr is not None:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in run(self, state)
340 patched_exception = self._patch_error(msg, e)
--> 341 raise patched_exception
342
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in run(self, state)
331 if isinstance(pass_inst, CompilerPass):
--> 332 self._runPass(idx, pass_inst, state)
333 else:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_lock.py in _acquire_compile_lock(*args, **kwargs)
31 with self:
---> 32 return func(*args, **kwargs)
33 return _acquire_compile_lock
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in _runPass(self, index, pss, internal_state)
290 with SimpleTimer() as pass_time:
--> 291 mutated |= check(pss.run_pass, internal_state)
292 with SimpleTimer() as finalize_time:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in check(func, compiler_state)
263 def check(func, compiler_state):
--> 264 mangled = func(compiler_state)
265 if mangled not in (True, False):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\typed_passes.py in run_pass(self, state)
441 # TODO: Pull this out into the pipeline
--> 442 NativeLowering().run_pass(state)
443 lowered = state['cr']
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\typed_passes.py in run_pass(self, state)
369 metadata=metadata)
--> 370 lower.lower()
371 if not flags.no_cpython_wrapper:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower(self)
216 # Materialize LLVM Module
--> 217 self.library.add_ir_module(self.module)
218
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\codegen.py in add_ir_module(self, ir_module)
205 ir = cgutils.normalize_ir_text(str(ir_module))
--> 206 ll_module = ll.parse_assembly(ir)
207 ll_module.name = ir_module.name
~\AppData\Local\Continuum\anaconda3\lib\site-packages\llvmlite\binding\module.py in parse_assembly(llvmir, context)
24 mod.close()
---> 25 raise RuntimeError("LLVM IR parsing error\n{0}".format(errmsg))
26 return mod
RuntimeError: Failed in nopython mode pipeline (step: nopython mode backend)
LLVM IR parsing error
<string>:4079:36: error: '%.2747' defined with type 'i64' but expected 'i32'
%".2748" = icmp eq i32 %".2746", %".2747"
^
During handling of the above exception, another exception occurred:
LoweringError Traceback (most recent call last)
<ipython-input-10-a83dc5279093> in <module>
----> 1 sc.pp.calculate_qc_metrics(adata, qc_vars=["mt"], inplace=True)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py in calculate_qc_metrics(adata, expr_type, var_type, qc_vars, percent_top, layer, use_raw, inplace, log1p, parallel)
294 inplace=inplace,
295 X=X,
--> 296 log1p=log1p,
297 )
298 var_metrics = describe_var(
~\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py in describe_obs(adata, expr_type, var_type, qc_vars, percent_top, layer, use_raw, log1p, inplace, X, parallel)
112 if percent_top:
113 percent_top = sorted(percent_top)
--> 114 proportions = top_segment_proportions(X, percent_top)
115 for i, n in enumerate(percent_top):
116 obs_metrics[f"pct_{expr_type}_in_top_{n}_{var_type}"] = (
~\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py in top_segment_proportions(mtx, ns)
377 mtx = csr_matrix(mtx)
378 return top_segment_proportions_sparse_csr(
--> 379 mtx.data, mtx.indptr, np.array(ns, dtype=np.int)
380 )
381 else:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in _compile_for_args(self, *args, **kws)
432 e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
433 # ignore the FULL_TRACEBACKS config, this needs reporting!
--> 434 raise e
435
436 def inspect_llvm(self, signature=None):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in _compile_for_args(self, *args, **kws)
365 argtypes.append(self.typeof_pyval(a))
366 try:
--> 367 return self.compile(tuple(argtypes))
368 except errors.ForceLiteralArg as e:
369 # Received request for compiler re-entry with the list of arguments
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_lock.py in _acquire_compile_lock(*args, **kwargs)
30 def _acquire_compile_lock(*args, **kwargs):
31 with self:
---> 32 return func(*args, **kwargs)
33 return _acquire_compile_lock
34
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in compile(self, sig)
806 self._cache_misses[sig] += 1
807 try:
--> 808 cres = self._compiler.compile(args, return_type)
809 except errors.ForceLiteralArg as e:
810 def folded(args, kws):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in compile(self, args, return_type)
76
77 def compile(self, args, return_type):
---> 78 status, retval = self._compile_cached(args, return_type)
79 if status:
80 return retval
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in _compile_cached(self, args, return_type)
90
91 try:
---> 92 retval = self._compile_core(args, return_type)
93 except errors.TypingError as e:
94 self._failed_cache[key] = e
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\dispatcher.py in _compile_core(self, args, return_type)
108 args=args, return_type=return_type,
109 flags=flags, locals=self.locals,
--> 110 pipeline_class=self.pipeline_class)
111 # Check typing error if object mode is used
112 if cres.typing_error is not None and not flags.enable_pyobject:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
601 pipeline = pipeline_class(typingctx, targetctx, library,
602 args, return_type, flags, locals)
--> 603 return pipeline.compile_extra(func)
604
605
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in compile_extra(self, func)
337 self.state.lifted = ()
338 self.state.lifted_from = None
--> 339 return self._compile_bytecode()
340
341 def compile_ir(self, func_ir, lifted=(), lifted_from=None):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_bytecode(self)
399 """
400 assert self.state.func_ir is None
--> 401 return self._compile_core()
402
403 def _compile_ir(self):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_core(self)
379 self.state.status.fail_reason = e
380 if is_final_pipeline:
--> 381 raise e
382 else:
383 raise CompilerError("All available pipelines exhausted")
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler.py in _compile_core(self)
370 res = None
371 try:
--> 372 pm.run(self.state)
373 if self.state.cr is not None:
374 break
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in run(self, state)
339 (self.pipeline_name, pass_desc)
340 patched_exception = self._patch_error(msg, e)
--> 341 raise patched_exception
342
343 def dependency_analysis(self):
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in run(self, state)
330 pass_inst = _pass_registry.get(pss).pass_inst
331 if isinstance(pass_inst, CompilerPass):
--> 332 self._runPass(idx, pass_inst, state)
333 else:
334 raise BaseException("Legacy pass in use")
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_lock.py in _acquire_compile_lock(*args, **kwargs)
30 def _acquire_compile_lock(*args, **kwargs):
31 with self:
---> 32 return func(*args, **kwargs)
33 return _acquire_compile_lock
34
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in _runPass(self, index, pss, internal_state)
289 mutated |= check(pss.run_initialization, internal_state)
290 with SimpleTimer() as pass_time:
--> 291 mutated |= check(pss.run_pass, internal_state)
292 with SimpleTimer() as finalize_time:
293 mutated |= check(pss.run_finalizer, internal_state)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\compiler_machinery.py in check(func, compiler_state)
262
263 def check(func, compiler_state):
--> 264 mangled = func(compiler_state)
265 if mangled not in (True, False):
266 msg = ("CompilerPass implementations should return True/False. "
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\typed_passes.py in run_pass(self, state)
440
441 # TODO: Pull this out into the pipeline
--> 442 NativeLowering().run_pass(state)
443 lowered = state['cr']
444 signature = typing.signature(state.return_type, *state.args)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\typed_passes.py in run_pass(self, state)
368 lower = lowering.Lower(targetctx, library, fndesc, interp,
369 metadata=metadata)
--> 370 lower.lower()
371 if not flags.no_cpython_wrapper:
372 lower.create_cpython_wrapper(flags.release_gil)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower(self)
177 if self.generator_info is None:
178 self.genlower = None
--> 179 self.lower_normal_function(self.fndesc)
180 else:
181 self.genlower = self.GeneratorLower(self)
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower_normal_function(self, fndesc)
231 # Init argument values
232 self.extract_function_arguments()
--> 233 entry_block_tail = self.lower_function_body()
234
235 # Close tail of entry block
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower_function_body(self)
257 bb = self.blkmap[offset]
258 self.builder.position_at_end(bb)
--> 259 self.lower_block(block)
260 self.post_lower()
261 return entry_block_tail
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\lowering.py in lower_block(self, block)
271 with new_error_context('lowering "{inst}" at {loc}', inst=inst,
272 loc=self.loc, errcls_=defaulterrcls):
--> 273 self.lower_inst(inst)
274 self.post_block(block)
275
~\AppData\Local\Continuum\anaconda3\lib\contextlib.py in __exit__(self, type, value, traceback)
128 value = type()
129 try:
--> 130 self.gen.throw(type, value, traceback)
131 except StopIteration as exc:
132 # Suppress StopIteration *unless* it's the same exception that
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\errors.py in new_error_context(fmt_, *args, **kwargs)
750 newerr = errcls(e).add_context(_format_msg(fmt_, args, kwargs))
751 tb = sys.exc_info()[2] if numba.core.config.FULL_TRACEBACKS else None
--> 752 reraise(type(newerr), newerr, tb)
753
754
~\AppData\Local\Continuum\anaconda3\lib\site-packages\numba\core\utils.py in reraise(tp, value, tb)
79 if value.__traceback__ is not tb:
80 raise value.with_traceback(tb)
---> 81 raise value
82
83
LoweringError: Failed in nopython mode pipeline (step: nopython mode backend)
Failed in nopython mode pipeline (step: nopython mode backend)
LLVM IR parsing error
<string>:4079:36: error: '%.2747' defined with type 'i64' but expected 'i32'
%".2748" = icmp eq i32 %".2746", %".2747"
^
File "..\..\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py", line 412:
def top_segment_proportions_sparse_csr(data, indptr, ns):
<source elided>
partitioned = np.zeros((indptr.size - 1, maxidx), dtype=data.dtype)
for i in numba.prange(indptr.size - 1):
^
During: lowering "id=13[LoopNest(index_variable = parfor_index.264, range = (0, $122binary_subtract.5, 1))]{130: <ir.Block at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (412)>, 400: <ir.Block at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (418)>, 402: <ir.Block at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (419)>, 276: <ir.Block at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (416)>, 318: <ir.Block at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (417)>}Var(parfor_index.264, _qc.py:412)" at C:\Users\tpeng\AppData\Local\Continuum\anaconda3\lib\site-packages\scanpy\preprocessing\_qc.py (412)
The package version is as follows:
scanpy==1.5.1 anndata==0.7.4 umap==0.4.6 numpy==1.18.5 scipy==1.5.0 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 python-igraph==0.7.1+5.3b99dbf6 leidenalg==0.7.0
Issue Analytics
- State:
- Created 3 years ago
- Comments:16 (9 by maintainers)
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It all works NOW! I appreciate your help!
It all works NOW! I appreciate your help!