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Genomepy install gets stuck #245

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DavideBrex opened this issue Jan 18, 2024 · 0 comments
Open

Genomepy install gets stuck #245

DavideBrex opened this issue Jan 18, 2024 · 0 comments

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@DavideBrex
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DavideBrex commented Jan 18, 2024

Hi,
Thank you for this helpful tool!
I run it in a snakemake pipeline with all the tools within a singularity container. A rule of the pipeline downloads the mm10 genome. When I execute the workflow locally, it works fine. However, if I run it on the university server, it gets stuck indefinitely and does not download the genome. Also, it does not output any line, so it has yet even to start the download.
I do not understand this behaviour. After a while that is stuck there, if I stop the pipeline, i get this error ( I do not know if it can be helpful). Do you have any ideas about what is happening? Thank you!

Traceback (most recent call last):
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/filelock/_unix.py", line 43, in _acquire
    fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB)
OSError: [Errno 37] No locks available

During handling of the above exception, another exception occurred:


Traceback (most recent call last):
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/bin/genomepy", line 7, in <module>
    from genomepy.cli import cli
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/genomepy/__init__.py", line 10, in <module
>
    from genomepy.annotation import Annotation, query_mygene
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/genomepy/annotation/__init__.py", line 11,
 in <module>
    from genomepy.annotation.mygene import _map_genes, query_mygene
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/genomepy/annotation/mygene.py", line 10, i
n <module>
    from genomepy.caching import cache_exp_other, disk_cache, lock
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/genomepy/caching.py", line 38, in <module>
    with lock:
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/filelock/_api.py", line 297, in __enter__
    self.acquire()
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/filelock/_api.py", line 255, in acquire
    self._acquire()
  File "/conda-envs/cd74cc1a40933954d4a4e18731a9e5fd/lib/python3.11/site-packages/filelock/_unix.py", line 45, in _acquire
    os.close(fd)
KeyboardInterrupt
@DavideBrex DavideBrex changed the title Genompepy install gets stuck Genomepy install gets stuck Jan 19, 2024
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