I am currently attempting to analyze the images from a 96-well plate in the Cell Painting format. I am using the following pipeline from Bray et al. Nat Protoc, 2016, 11, 1757-1774 (doi:10.1038/nprot.2016.105). 211analysis.cppipe (39.4 KB) in Cell Profiler 2.1.1.
However I am receiving the following error after analyzing a few image sets.
Traceback (most recent call last): File "cellprofiler\pipeline.pyc", line 1934, in run_image_set File "cellprofiler\modules\exporttodatabase.pyc", line 1754, in run File "cellprofiler\modules\exporttodatabase.pyc", line 2917, in write_data_to_db File "cellprofiler\modules\exporttodatabase.pyc", line 262, in execute File "MySQLdb\cursors.pyc", line 174, in execute File "MySQLdb\connections.pyc", line 36, in defaulterrorhandler OperationalError: (1205, 'Lock wait timeout exceeded; try restarting transaction')
I found something reported on the issue:
However we are not running on a cluster. The PC is running 16 workers (16 core CPU). Is this causing the issue?
I can press “Continue Processing…”, and if I tick off “Don’t show this error again” the analysis will proceed, but I am not certain that everything is then writting correctly to the database.
Is the issue solved in Cell Profiler 2.2.0, or is there another fix to the problem?
With Kind Regards