I’m new to cellprofiler so I’m trying to learn batch processing with the simplest example I could think of. So I’m trying to port the very first HumanCells example  to run in batch mode.
I’m running version 2.2.0rc3 on a mac  and after getting java set up I can do the whole example via the GUI and generate valid output images. But then I export the pipeline and the Image_file_list and try to run from the command line and can’t seem to get things working even though I think I have the paths correct.
Here’s the command line I use:
./CellProfiler -r -c -p /tmp/humans/ExampleHuman.cppipe -o /tmp/humans/output --data-file=/tmp/humans/Image_file_list.csv -L 10
I get a very verbose output with lots of apparently unrelated java errors (they also appear in the GUI mode where this example works).
The key error message appears to be this one:
CP-JAVA 11:54:47.283 [Thread-1] WARN o.c.imageset.ChannelFilter - Empty image set list: no images passed the filtering criteria.
I’ve seen references to others seeing this problem but never an answer about the root cause.
I’ve uploaded the pipeline and other data here . Would someone be able to try this and point me in the right direction?
Thanks in advance!
 $ ./CellProfiler --version
Mar 25 12:01:03 CellProfiler : CellProfiler 2.2.0rc3
Mar 25 12:01:03 CellProfiler : Git b91da8e
Mar 25 12:01:03 CellProfiler : Version 20160308191757
Mar 25 12:01:03 CellProfiler : Built 2016-03-08T19:17:57