Unable to open database file


I’m sorry if this ends up posted twice… it seems that my original post did not go through.

I’m new to CellProflier (first project), so I’m hoping this is something dumb that I’ve overlooked. When I try to analyze my images, I get the following error messages:

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 2094, in prepare_run
File “cellprofiler\modules\exporttodatabase.pyc”, line 1577, in prepare_run
File “cellprofiler\modules\exporttodatabase.pyc”, line 304, in connect_sqlite
OperationalError: unable to open database file

Traceback (most recent call last):
File “analysis_worker.py”, line 367, in do_job
File “cellprofiler\measurements.pyc”, line 1767, in load_measurements_from_buffer
File “tempfile.pyc”, line 293, in mkstemp
File “tempfile.pyc”, line 228, in _mkstemp_inner
OSError: [Errno 13] Permission denied

I’ve attached the pipeline, please let me know if there is any other information you need!


EPI_EqUT_Ki67.cpproj (1.67 MB)

Hi Natalie,

Nothing looks amiss immediately. I would first check what your Default Output Directory is set to, since that is where ExportToDatabase is set to output to. Click on the “View Output Files” button at the bottom of your pipeline and check that you have write access to the Default Output Folder on your machine.

Let us know how it goes.