VEP plugin with PYTHON error

[loganylchen]

• MMSplice version:master(git clone from github)
• Python version:3.5
• Operating System: docker image

Description

I added MMSplice into VEP docker and ran it in the followed command, but it goes wrong.

I entered docker container

docker run -it -v `pwd`:`pwd` mmsplicedocker bash

What I Did

 vep -i test.vcf --plugin MMSplice --vcf --force  --offline --cache --dir path-to/VEP/ -o test2.vcf --fasta path-to/human_g1k_v37.fasta

OUTPUT

/usr/local/lib/python3.6/dist-packages/concise/utils/plot.py:115: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
  min_coords = np.vstack(data.min(0) for data in polygons_data).min(0)
/usr/local/lib/python3.6/dist-packages/concise/utils/plot.py:116: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
  max_coords = np.vstack(data.max(0) for data in polygons_data).max(0)
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
2019-07-26 02:15:11,327 [WARNING] From /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
2019-07-26 02:15:11.429590: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 AVX512F FMA
2019-07-26 02:15:11.815407: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2294595000 Hz
2019-07-26 02:15:12.031385: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x34b7bd0 executing computations on platform Host. Devices:
2019-07-26 02:15:12.031435: I tensorflow/compiler/xla/service/service.cc:158]   StreamExecutor device (0): <undefined>, <undefined>
/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py:292: UserWarning: No training configuration found in save file: the model was *not* compiled. Compile it manually.
  warnings.warn('No training configuration found in save file: '
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.
Instructions for updating:
Please use `rate` instead of `keep_prob`. Rate should be set to `rate = 1 - keep_prob`.
2019-07-26 02:15:13,066 [WARNING] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.
Instructions for updating:
Please use `rate` instead of `keep_prob`. Rate should be set to `rate = 1 - keep_prob`.
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/math_ops.py:3066: to_int32 (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.cast instead.
2019-07-26 02:15:13,494 [WARNING] From /usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/math_ops.py:3066: to_int32 (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.cast instead.
2019-07-26 02:15:18,974 [WARNING] None GT donor: 
2019-07-26 02:15:18,975 [WARNING] None AG acceptor: 
Use of uninitialized value in subtraction (-) at
    /opt/vep/src/Plugins/MMSplice.pm line 232, <__ANONIO__> line 200 (#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 in addition (+) at /opt/vep/src/Plugins/MMSplice.pm
    line 232, <__ANONIO__> line 200 (#1)
Use of uninitialized value in subtraction (-) at
    /opt/vep/src/Plugins/MMSplice.pm line 216, <__ANONIO__> line 200 (#1)
Use of uninitialized value in addition (+) at /opt/vep/src/Plugins/MMSplice.pm
    line 217, <__ANONIO__> line 200 (#1)
Use of uninitialized value in concatenation (.) or string at
    /opt/vep/src/Plugins/MMSplice.pm line 340, <__ANONIO__> line 200 (#1)
Traceback (most recent call last):
  File "/usr/local/bin/mmsplice", line 11, in <module>
    sys.exit(cli())
  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/mmsplice/main.py", line 32, in run
    variant = json.loads(sys.stdin.readline().strip())
  File "/usr/lib/python3.6/json/__init__.py", line 354, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.6/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.6/json/decoder.py", line 357, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 17 (char 16)
Use of uninitialized value $result in chomp at /opt/vep/src/Plugins/MMSplice.pm
    line 115, <GEN1> line 54 (#1)
Use of uninitialized value $result in string eq at
    /opt/vep/src/Plugins/MMSplice.pm line 116, <GEN1> line 54 (#1)

[s6juncheng]

Hi @btrspg, thanks for trying MMSplice. This seams related to our recent restructure of MMSplice package. You can use the older pypi version with pip install mmsplice==0.2.7, it should work.

[loganylchen]

Thanks for a quick reply, @s6juncheng I will try that.

[MuhammedHasan]

Thanks for reporting the issue. Our latest mmsplice release has caused the reported issue. Now, I have updated the vep plugin as well. VEP plugin and latest mmsplice should work fine.

Can you retry it from master branch?

[loganylchen]

@MuhammedHasan I have used the mmsplice==0.2.7, and it works fine. If the master branch was a stable release, maybe a new release number could be set, so that I can special my dockerfile version number as well.