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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Error when run ipyrad #456

Closed yexiaying199056 closed 2 years ago

yexiaying199056 commented 2 years ago

image I installed ipyrad in a conda environment, and can read the help information with "ipyrad -h", but with error when I tried to run it. Do you have any idea how to fix it? Thank you very much! Ye Xiaying

yexiaying199056 commented 2 years ago

with -d parameter, it shows like this: ipyrad [v.0.9.81] Interactive assembly and analysis of RAD-seq data

Encountered an Error. Message: KeyboardInterrupt: Parallel connection closed. ---------------------------------------------------------------------------KeyboardInterrupt Traceback (most recent call last)~/.conda/envs/rad/lib/python3.9/site-packages/ipyparallel/serialize/serialize.py in serialize_object(obj, buffer_threshold, item_threshold) 120 cobj[k] = c 121 else: --> 122 cobj = can(obj) 123 buffers.extend(_extract_buffers(cobj, buffer_threshold)) 124 ~/.conda/envs/rad/lib/python3.9/site-packages/ipyparallel/serialize/canning.py in can(obj) 396 # perform can_map imports, then try again 397 # this will usually only happen once --> 398 _import_mapping(can_map, _original_can_map) 399 return can(obj) 400 ~/.conda/envs/rad/lib/python3.9/site-packages/ipyparallel/serialize/canning.py in _import_mapping(mapping, original) 359 if isinstance(key, string_types): 360 try: --> 361 cls = import_item(key) 362 except Exception: 363 if original and key not in original: ~/.conda/envs/rad/lib/python3.9/site-packages/ipython_genutils/importstring.py in import_item(name) 29 # called with 'foo.bar....' 30 package, obj = parts ---> 31 module = import(package, fromlist=[obj]) 32 try: 33 pak = getattr(module, obj) ~/.conda/envs/rad/lib/python3.9/site-packages/numpy/init.py in 148 from . import _distributor_init 149 --> 150 from . import core 151 from .core import 152 from . import compat ~/.conda/envs/rad/lib/python3.9/site-packages/numpy/core/init.py in 20 21 try: ---> 22 from . import multiarray 23 except ImportError as exc: 24 import sys ~/.conda/envs/rad/lib/python3.9/site-packages/numpy/core/multiarray.py in 10 import warnings 11 ---> 12 from . import overrides 13 from . import _multiarray_umath 14 from ._multiarray_umath import # noqa: F403 ~/.conda/envs/rad/lib/python3.9/site-packages/numpy/core/overrides.py in 5 import textwrap 6 ----> 7 from numpy.core._multiarray_umath import ( 8 add_docstring, implement_array_function, _get_implementing_args) 9 from numpy.compat._inspect import getargspec KeyboardInterrupt:

isaacovercast commented 2 years ago

This looks like a very unusual issue with numpy which there are some suggestions for solving here:

https://github.com/numpy/numpy/issues/14868

This looks like an issue with your host machine and numpy. You might try adding -c 1 to the ipyrad command. You might also try some of the things suggested in the github issue I post above.

yexiaying199056 commented 2 years ago

Thank you very much! It ran successfully with parameter -c.