I’ve been working on a CellProfiler build for the cluster I’m working with (@allen_goodman might recognize me), and I’ve finally got a “working” build set up in a virtual environment that I’m currently trying to test to see if it’s functioning as intended. I’ve downloaded several of the example pipelines from the website, and I’m having some issues getting them to execute in headless mode. What I’ve tried so far is installing a local version to my desktop/laptop (from the git repo so as to be as close as possible to the cluster install), and importing those example pipelines, appending the CreateBatchFiles module to the end, and creating the .h5 file. However, I can’t actually execute the command generated by
cellprofiler --get-batch-commands Batch_data.h5
Anywhere, including on my local machine, where I generated the file. For example, using the basic Human Cells pipeline from the website, the output of the above command is this:
CellProfiler -c -r -p Batch_data.h5 -g ImageNumber=1
Even though they don’t appear to be grouped (but I’ll get to that in a second). If I run that command, either locally or on the cluster (with the amended paths), I get something like this:
Version: 2016-05-13T20:00:34 9cad7ea / 20160513200034 Pipeline saved with CellProfiler version 20160503134940 Times reported are CPU times for each module, not wall-clock time Uncaught exception in CellProfiler.py Traceback (most recent call last): File "/home/at237/CellProfiler_test/CPvenv/src/cellprofiler-master/cellprofiler/__main__.py", line 251, in main run_pipeline_headless(options, args) File "/home/at237/CellProfiler_test/CPvenv/src/cellprofiler-master/cellprofiler/__main__.py", line 898, in run_pipeline_headless initial_measurements=initial_measurements) File "/home/at237/CellProfiler_test/CPvenv/src/cellprofiler-master/cellprofiler/pipeline.py", line 1684, in run initial_measurements=measurements): File "/home/at237/CellProfiler_test/CPvenv/src/cellprofiler-master/cellprofiler/pipeline.py", line 1796, in run_with_yield in group(workspace): File "/home/at237/CellProfiler_test/CPvenv/src/cellprofiler-master/cellprofiler/pipeline.py", line 1714, in group ", ".join(grouping.keys()), ", ".join(keys))) ValueError: The grouping keys specified on the command line (ImageNumber) must be the same as those defined by the modules in the pipeline ()
And if I omit the -g flag, I get this regurgitation of java exceptions (which I can paste if requested). I’ve tried messing with the groups input module and what I pass to -g (somewhat blindly, I admit), but I can’t seem to generate a working command. Any ideas?