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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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I use run_gubbins.py -P to test and get an error, but I don't know how to solve it, please help #346

Closed xianglongwei closed 2 years ago

xianglongwei commented 2 years ago 
raise errors[0]

numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend) No implementation of function Function() found for signature:

contains(array(int32, 1d, A), int32)

There are 18 candidate implementations:

During: typing of intrinsic-call at /NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py (312)

File "../../../../../miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py", line 312: def reconstruct_alleles(reconstructed_alleles,

for node_index in postordered_nodes:
    if node_index in leaf_nodes:
    ^

Environment centos linux 64, use conda to install gubbins_3.2.1 image

xianglongwei commented 2 years ago

Traceback (most recent call last): File "/NAS/home/chenyx/miniconda3/bin/run_gubbins.py", line 33, in sys.exit(load_entry_point('gubbins==3.1.4', 'console_scripts', 'run_gubbins.py')()) File "/NAS/home/chenyx/miniconda3/bin/run_gubbins.py", line 25, in importlib_load_entry_point return next(matches).load() File "/NAS/home/chenyx/miniconda3/lib/python3.8/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/NAS/home/chenyx/miniconda3/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 961, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 975, in _find_and_load_unlocked File "", line 671, in _load_unlocked File "", line 783, in exec_module File "", line 219, in _call_with_frames_removed File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/init.py", line 16, in from gubbins import common File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/common.py", line 43, in from gubbins.pyjar import jar, read_alignment, get_base_patterns File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py", line 326, in def reconstruct_alleles(reconstructed_alleles, File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/decorators.py", line 218, in wrapper disp.compile(sig) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_lock.py", line 32, in _acquire_compile_lock return func(*args, *kwargs) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 819, in compile cres = self._compiler.compile(args, return_type) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 82, in compile raise retval File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 92, in _compile_cached retval = self._compile_core(args, return_type) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 105, in _compile_core cres = compiler.compile_extra(self.targetdescr.typing_context, File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 625, in compile_extra return pipeline.compile_extra(func) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 361, in compile_extra return self._compile_bytecode() File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 423, in _compile_bytecode return self._compile_core() File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 403, in _compile_core raise e File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 394, in _compile_core pm.run(self.state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 341, in run raise patched_exception File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 332, in run self._runPass(idx, pass_inst, state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_lock.py", line 32, in _acquire_compile_lock return func(args, **kwargs) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 291, in _runPass mutated |= check(pss.run_pass, internal_state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 264, in check mangled = func(compiler_state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typed_passes.py", line 92, in run_pass typemap, return_type, calltypes = type_inference_stage( File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typed_passes.py", line 70, in type_inference_stage infer.propagate(raise_errors=raise_errors) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typeinfer.py", line 1071, in propagate raise errors[0] numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend) No implementation of function Function() found for signature:

contains(array(int32, 1d, A), int32)

There are 18 candidate implementations:

During: typing of intrinsic-call at /NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py (334)

File "../../../../../miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py", line 334: def reconstruct_alleles(reconstructed_alleles,

for node_index in postordered_nodes:
    if node_index in leaf_nodes:

I lowered the version, same error

nickjcroucher commented 2 years ago

Does this still happen if you upgrade to v3.2.1?

From: aisono @.> Sent: Thursday, August 18, 2022 9:28:02 AM To: nickjcroucher/gubbins @.> Cc: Subscribed @.***> Subject: Re: [nickjcroucher/gubbins] I use run_gubbins.py -P to test and get an error, but I don't know how to solve it, please help (Issue #346)

Traceback (most recent call last): File "/NAS/home/chenyx/miniconda3/bin/run_gubbins.py", line 33, in sys.exit(load_entry_point('gubbins==3.1.4', 'console_scripts', 'run_gubbins.py')()) File "/NAS/home/chenyx/miniconda3/bin/run_gubbins.py", line 25, in importlib_load_entry_point return next(matches).load() File "/NAS/home/chenyx/miniconda3/lib/python3.8/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/NAS/home/chenyx/miniconda3/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 961, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 975, in _find_and_load_unlocked File "", line 671, in _load_unlocked File "", line 783, in exec_module File "", line 219, in _call_with_frames_removed File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/init.py", line 16, in from gubbins import common File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/common.py", line 43, in from gubbins.pyjar import jar, read_alignment, get_base_patterns File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py", line 326, in def reconstruct_alleles(reconstructed_alleles, File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/decorators.py", line 218, in wrapper disp.compile(sig) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_lock.py", line 32, in _acquire_compile_lock return func(*args, *kwargs) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 819, in compile cres = self._compiler.compile(args, return_type) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 82, in compile raise retval File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 92, in _compile_cached retval = self._compile_core(args, return_type) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/dispatcher.py", line 105, in _compile_core cres = compiler.compile_extra(self.targetdescr.typing_context, File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 625, in compile_extra return pipeline.compile_extra(func) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 361, in compile_extra return self._compile_bytecode() File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 423, in _compile_bytecode return self._compile_core() File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 403, in _compile_core raise e File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler.py", line 394, in _compile_core pm.run(self.state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 341, in run raise patched_exception File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 332, in run self._runPass(idx, pass_inst, state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_lock.py", line 32, in _acquire_compile_lock return func(args, **kwargs) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 291, in _runPass mutated |= check(pss.run_pass, internal_state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 264, in check mangled = func(compiler_state) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typed_passes.py", line 92, in run_pass typemap, return_type, calltypes = type_inference_stage( File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typed_passes.py", line 70, in type_inference_stage infer.propagate(raise_errors=raise_errors) File "/NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/numba/core/typeinfer.py", line 1071, in propagate raise errors[0] numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend) No implementation of function Function() found for signature:

contains(array(int32, 1d, A), int32)

There are 18 candidate implementations:

During: typing of intrinsic-call at /NAS/home/chenyx/miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py (334)

File "../../../../../miniconda3/lib/python3.8/site-packages/gubbins/pyjar.py", line 334: def reconstruct_alleles(reconstructed_alleles,

for node_index in postordered_nodes: if node_index in leaf_nodes:

I lowered the version, same error

— Reply to this email directly, view it on GitHubhttps://github.com/nickjcroucher/gubbins/issues/346#issuecomment-1219186710, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD6PWQ73H3L6DJFHQBLPFEDVZXXZFANCNFSM564HYPLA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

xianglongwei commented 2 years ago

Yes 3.2.1, I currently use the gubbins-3.1.4-py38h390ddb8_0.tar.bz2 version and it runs normally, and the versions after gubbins-3.1.4-py38h390ddb8_0.tar.bz2 have the same problem

nickjcroucher commented 2 years ago

It looks as though some of version 3.1.4 is still lingering can you try a clean install in a new conda env?

From: aisono @.> Sent: Thursday, August 18, 2022 10:13:30 AM To: nickjcroucher/gubbins @.> Cc: Croucher, Nicholas J @.>; Comment @.> Subject: Re: [nickjcroucher/gubbins] I use run_gubbins.py -P to test and get an error, but I don't know how to solve it, please help (Issue #346)

Yes 3.2.1, I currently use the gubbins-3.1.4-py38h390ddb8_0.tar.bz2 version and it runs normally, and the versions after gubbins-3.1.4-py38h390ddb8_0.tar.bz2 have the same problem

— Reply to this email directly, view it on GitHubhttps://github.com/nickjcroucher/gubbins/issues/346#issuecomment-1219233435, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD6PWQ46LSPOMOEBEPPJKQLVZX5DVANCNFSM564HYPLA. You are receiving this because you commented.Message ID: @.***>

xianglongwei commented 2 years ago

I'm very sorry, the installation operation cannot be performed at the moment. It took me 2 days to install it and it can be used. If it is solved in the future, please let me know. thanks

nickjcroucher commented 2 years ago

OK - beware that the error includes the line: sys.exit(load_entry_point('gubbins==3.1.4', 'console_scripts', 'run_gubbins.py')()) indicating version 3.1.4 is still being used for some aspects of the analysis - this is likely not compatible with the 3.2.1 installation. I suspect the error reflects this mismatch in installed packages rather than a bug with the current release.