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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Error: sqlite3 unable to open database file #183

Open blasks opened 4 years ago

blasks commented 4 years ago

I've had a number of troubles getting dammit installed and working on my MacOS environment. I have miniconda3 installed and download dammit into a new environment using the following:

conda create -n dammit python=3.6
conda activate dammit
conda install dammit

With this, conda takes several minutes to solve the environment. Once everything is downloaded and installed, which busco returns nothing despite conda saying that it was downloaded and installed. Then when I try to run dammit databases --full --database-dir <directory/path> --busco-group protists --install I get the following error:

Traceback (most recent call last):
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/doit_cmd.py", line 177, in run
    return command.parse_execute(args)
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/cmd_base.py", line 127, in parse_execute
    return self.execute(params, args)
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/cmd_base.py", line 406, in execute
    db_class, params['dep_file'], checker_cls)
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/dependency.py", line 475, in __init__
    self.backend = db_class(backend_name)
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/dependency.py", line 236, in __init__
    self._conn = self._sqlite3(self.name)
  File "/opt/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/dependency.py", line 261, in _sqlite3
    isolation_level='DEFERRED')
sqlite3.OperationalError: unable to open database file

I checked and sqlite3 is properly installed in the environment. I've been able to run at least the non-busco steps of the pipeline previously, but now I can't even do that because of this error.

schippmeister commented 3 years ago

Same problem for me, though I am using python 3.7

camillescott commented 3 years ago

Sorry for missing this issue originally. dammit v1.x is not compatible with MacOS due to issues with pinned dependencies. v2 will likely work on MacOS, but the compatibility is a work in progress.

mptrsen commented 3 years ago

Hi Camille! I'm having the same issue with v1.2, but on Linux. Same installation procedure.

taylorreiter commented 12 months ago

I also received this error on linux, but only when I tried to specify an output directory for the database. If I let it download the databases to the default path, no error occurs.