Skip to content

OverflowError: signed integer is greater than maximum #70

Description

@abrozzi

Hi,

always the same error. I tried both on my Mac (16 GB RAM) and on Unix server:

(base) abrozzi@MBP-di-Stefano ~ % docker run -v /Users/abrozzi/gvgh:/data phelimb/bigsi bigsi bulk_search -c /data/config.yaml /data/C_RS04605.fas
Traceback (most recent call last):
  File "/usr/local/bin/bigsi", line 11, in <module>
    load_entry_point('bigsi==0.3.5', 'console_scripts', 'bigsi')()
  File "/usr/local/lib/python3.7/dist-packages/bigsi-0.3.5-py3.7.egg/bigsi/__main__.py", line 307, in main
  File "/usr/local/lib/python3.7/dist-packages/hug/api.py", line 399, in __call__
    result = self.commands.get(command)()
  File "/usr/local/lib/python3.7/dist-packages/hug/interface.py", line 546, in __call__
    raise exception
  File "/usr/local/lib/python3.7/dist-packages/hug/interface.py", line 542, in __call__
    result = self.output(self.interface(**pass_to_function), context)
  File "/usr/local/lib/python3.7/dist-packages/hug/interface.py", line 100, in __call__
    return __hug_internal_self._function(*args, **kwargs)
  File "/usr/local/lib/python3.7/dist-packages/bigsi-0.3.5-py3.7.egg/bigsi/__main__.py", line 258, in bulk_search
  File "/usr/local/lib/python3.7/dist-packages/bigsi-0.3.5-py3.7.egg/bigsi/graph/bigsi.py", line 131, in __init__
  File "/usr/local/lib/python3.7/dist-packages/bigsi-0.3.5-py3.7.egg/bigsi/storage/__init__.py", line 19, in get_storage
  File "/usr/local/lib/python3.7/dist-packages/bigsi-0.3.5-py3.7.egg/bigsi/storage/berkeleydb.py", line 15, in __init__
  File "/usr/local/lib/python3.7/dist-packages/bsddb3/__init__.py", line 326, in hashopen
    e = _openDBEnv(cachesize)
  File "/usr/local/lib/python3.7/dist-packages/bsddb3/__init__.py", line 379, in _openDBEnv
    e.set_cachesize(0, cachesize)
OverflowError: signed integer is greater than maximum

I downloaded the index10k from https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000499

Where I am wrong?

Thank you in advance!

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions