self._sem._semlock._get_value() not implemented error

[ardakdemir]

Would this error cause a problem with the returned values ? Or should I just ignore it?

 # Raises NotImplementedError on Mac OSX because of broken sem_getvalue()
    return self._maxsize - self._sem._semlock._get_value()

[PengNi]

Hi @ardakdemir , do you have a more complete log? I didn't met this error before.

[ardakdemir]

I copied that line from the source code itself.

The complete log looks as follows:

1 fast5 files in total..
parse the motifs string..
read genome reference file..
write_process started..
Process Process-1:
Traceback (most recent call last):
  File
"/Users/ardaakdemir/anaconda3/envs/deepsignalenv/lib/python3.6/multiprocessing/process.py",
line 258, in _bootstrap
    self.run()
  File
"/Users/ardaakdemir/anaconda3/envs/deepsignalenv/lib/python3.6/multiprocessing/process.py",
line 93, in run
    self._target(*self._args, **self._kwargs)
  File
"/Users/ardaakdemir/anaconda3/envs/deepsignalenv/lib/python3.6/site-packages/deepsignal-0.1.5-py3.6.egg/deepsignal/extract_features.py",
line 280, in get_a_batch_features_str
    while featurestr_q.qsize() > queen_size_border:
  File
"/Users/ardaakdemir/anaconda3/envs/deepsignalenv/lib/python3.6/multiprocessing/queues.py",
line 117, in qsize
    return self._maxsize - self._sem._semlock._get_value()
NotImplementedError
finishing the write_process.```

Peng Ni <notifications@github.com>, 12 Eki 2019 Cmt, 21:22 tarihinde şunu
yazdı:

> Hi @ardakdemir <https://github.com/ardakdemir> , do you have a more
> complete log? I didn't met this error before.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
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[PengNi]

It looks like a bug. It maybe occured by too few fast5 files as input. We'll do some tests and fix it ASAP.

1 fast5 files in total..

Meanwhile, I think you can try to use more fast5 files as input, or try to use less processors (--nproc), or decrease the --f5_batch_num (default 100).

[PengNi]

Hi @ardakdemir , it turns out that it is a macos/multiprocessing issue. I fixed it in develop branch (@285c87a) as vterron/lemon@9ca6b4b. Please tell me If you have any other problem.

[ardakdemir]

Thanks a lot I will check the develop branch!

Peng Ni notifications@github.com, 21 Eki 2019 Pzt, 09:28 tarihinde şunu yazdı:

Hi @ardakdemir https://github.com/ardakdemir , it turns out that it is a macos/multiprocessing issue. I fixed it in develop branch (@285c87a https://github.com/bioinfomaticsCSU/deepsignal/commit/285c87ace46d905f4a5740e8e0f4a5ad27b27381) as vterron/lemon@9ca6b4b https://github.com/vterron/lemon/commit/9ca6b4b1212228dbd4f69b88aaf88b12952d7d6f. Please tell me If you have any other problem.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bioinfomaticsCSU/deepsignal/issues/21?email_source=notifications&email_token=AC5IHLQB4VQJX5UYHDTO3I3QPTZRPA5CNFSM4JACUPF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBYX5PQ#issuecomment-544308926, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC5IHLW734O3OURIPFDKDU3QPTZRPANCNFSM4JACUPFQ .