Problem with --data-files and --file-list

Dear community,
I try to launch a simple CorrectIllumintation pipeline using CellProfiler 3.1.3 installed on a linux environment (RHEL 7.6 with LSF 9.1.3).
My pipeline consists of 4 modules:

  • loadData
  • CorrectIlluminationCalculate
  • SaveImages
  • CreateBatchFiles

When run directly through the GUI (without CreateBatchFile), it works perfectly. When run through this command line:

cellprofiler -c -r -p /Instruments/microscopy/2-Prog/CellProfiler/illum_out/Batch_data.h5 --plugins-directory /Software/python/Anaconda-5.2.0-cellprof/plugins/CellProfiler

it also run correctly using the csv I specified while running the pipeline thourgh the GUI. But when I try to specify the csv in the command line it fails (also if I use --data-file=…):

cellprofiler -c -r -p /Instruments/microscopy/2-Prog/CellProfiler/illum_out/Batch_data.h5 --plugins-directory /Software/python/Anaconda-5.2.0-cellprof/plugins/CellProfiler --data-file /Instruments/microscopy/2-Prog/CellProfiler/illum_out/Illum_FileList_24418_Test.csv

The error is this one:

Error detected during run of module LoadData
Traceback (most recent call last):
  File "/Software/cellprof/CellProfiler-master/cellprofiler/", line 1779, in run_with_yield
    self.run_module(module, workspace)
  File "/Software/cellprof/CellProfiler-master/cellprofiler/", line 2031, in run_module
  File "/Software/cellprof/CellProfiler-master/cellprofiler/modules/", line 1205, in run
    value = m.get_measurement(cellprofiler.measurement.IMAGE, feature_name)
  File "/Software/cellprof/CellProfiler-master/cellprofiler/", line 963, in get_measurement
    vals = self.hdf5_dict[object_name, feature_name, image_set_number]
  File "/Software/cellprof/CellProfiler-master/cellprofiler/utilities/", line 374, in __getitem__
    result = self[object_name, feature_name, [num_idx]]
  File "/Software/cellprof/CellProfiler-master/cellprofiler/utilities/", line 379, in __getitem__
    assert feature_exists, "Feature {} for {} does not exist".format(feature_name, object_name)
AssertionError: Feature Group_Number,"Group_Index","URL_raw","PathName_raw","FileName_raw","Series_raw","Frame_raw","Channel_raw","Metadata_Barcode","Metadata_ChannelNumber","Metadata_Date","Metadata_FileLocation","Metadata_Frame","Metadata_Plate","Metadata_PlateID","Metadata_Series","Metadata_Site","Metadata_Well" for Image does not exist
Wed Apr 17 11:37:13 2019: Image # 1, module LoadData # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs

Just to add that the csv I try to specify is just a longer version of the one I specify through the GUI so it suspect it is not due to a badly defined csv.

When I try the same pipeline using the Images/Metadata/Names/Groups and the --file-list switch, there is no error but it just use the list of files specified in the GUI and not the list specified in the csv.

Could you please points me to the error or to explain me better how to use the switches ?
Thank you for your help,

N.B: I opened an issue on CellProfiler GitHub for the same question.

The issue was solved by someone on the GitHub page… I shouldn’t have linked the batch file as it already contains the list of files embedded in the h5 file but linked the .cpproj directly.
The correct call is then:

cellprofiler -c -r -p /Instruments/microscopy/2-Prog/CellProfiler/illum_out/analysis.cpproj --plugins-directory /Software/python/Anaconda-5.2.0-cellprof/plugins/CellProfiler --data-file=/Instruments/microscopy/2-Prog/CellProfiler/illum_out/Illum_FileList_24418_Test.csv