MySQL Error: Row size too large


Hi, first of all: thanks a lot for making this brillant software open-source and for maintaining it. This effort is highly appreciated!

We are just getting started with cell painting and with using CP and CPA and are struggling with some technical issues.
When I try to process a very small set of images (10 wells , 9 sites, 5 channels) into a MySQL database, I get the following error when the first data is being written:

INFO:cellprofiler.analysis:Worker 2: OperationalError: (1118, 'Row size too large (> 8126). Changing some columns to TEXT or BLOB or using ROW_FORMAT=DYNAMIC or ROW_FORMAT=COMPRESSED may help. In current row format, BLOB prefix of 768 bytes is stored inline.')

Since no further information is given, I am not quite sure what could be changed.
I have attached the project file.
project.cpproj (1.0 MB)

This happens with the following setup:
CP cloned from GitHub, running in Anaconda with Python 2.7 on Kubuntu 16.10
MySQL server: 5.5.53 on Ubuntu 14.04

Many thanks in advance for your help!

Kind regards,

CPA Image Gallery only shows Coloured Squares

Hi Axel,
Can you try turning off the calculation of the per-well medians and standard deviations in ExportToDatabase before running it? Those often cause you to have too many columns for MySQL, which IIRC causes the error you’re seeing. You can always recreate the medians and standard deviations later for the features you care about.


Hi Beth,

turning off the calculation of the per-well medians and standard deviations made the error disappear.
Thanks a lot for the very fast answer!

Kind regards,