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ValueError: numpy.ndarray size changed, may indicate binary incompatibility. #61

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zyh4482 opened this issue Apr 12, 2022 · 0 comments

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@zyh4482
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zyh4482 commented Apr 12, 2022

When I tried to use MMSplice plugin, it comes with error message:

running code: 
vep -i ~/data/in.vcf.gz --vcf --no_stats -o ~/data/out.vcf --cache --plugin MMSplice
2022-04-12 17:44:48.311714: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-04-12 17:44:48.311754: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Traceback (most recent call last):
  File "/home/tomas/anaconda3/bin/mmsplice", line 5, in <module>
    from mmsplice.main import cli
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/mmsplice/__init__.py", line 8, in <module>
    from mmsplice.mmsplice import MMSplice, \
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/mmsplice/mmsplice.py", line 10, in <module>
    from mmsplice.utils import logit, predict_deltaLogitPsi, \
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/mmsplice/utils.py", line 4, in <module>
    from kipoiseq.dataclasses import Variant, Interval
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/kipoiseq/__init__.py", line 11, in <module>
    from . import dataloaders
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/kipoiseq/dataloaders/__init__.py", line 1, in <module>
    from .sequence import *
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/kipoiseq/dataloaders/sequence.py", line 11, in <module>
    from kipoiseq.extractors import FastaStringExtractor
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/kipoiseq/extractors/__init__.py", line 4, in <module>
    from .vcf import *
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/kipoiseq/extractors/vcf.py", line 12, in <module>
    from cyvcf2 import VCF
  File "/home/tomas/anaconda3/lib/python3.8/site-packages/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
  File "cyvcf2/cyvcf2.pyx", line 1, in init cyvcf2.cyvcf2
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Use of uninitialized value $result in chomp at
	/home/tomas/.vep/Plugins/MMSplice.pm line 117, <GEN1> line 25 (#1)
    (W uninitialized) An undefined value was used as if it were already
    defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.
    To suppress this warning assign a defined value to your variables.
    
    To help you figure out what was undefined, perl will try to tell you
    the name of the variable (if any) that was undefined.  In some cases
    it cannot do this, so it also tells you what operation you used the
    undefined value in.  Note, however, that perl optimizes your program
    and the operation displayed in the warning may not necessarily appear
    literally in your program.  For example, "that $foo" is usually
    optimized into "that " . $foo, and the warning will refer to the
    concatenation (.) operator, even though there is no . in
    your program.
    
Use of uninitialized value $result in string eq at
	/home/tomas/.vep/Plugins/MMSplice.pm line 118, <GEN1> line 25 (#1)

What does this error suggest?
Could you please help me with it? Thanks

@zyh4482 zyh4482 changed the title MSG: homo_sapiens is not a valid species name ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Apr 12, 2022
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