Unable to create batch files

Hi all,

I am having problems creating a batch file for my pipeline. I am trying to use a remote computer to generate a batch file on our cluster, which is also where my images are saved. I can run the pipeline without the CreateBatchFiles module and everything runs fine. However, when I include the CreateBatchFiles module, I get the following error message:

There was a problem running the analysis module CreateBatchFiles which is number 14. Error using ==> strrep
Cell elements must be character arrays.

CreateBatchFiles in C:\Program Files\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\Modules\CreateBatchFiles.m (128)
AnalyzeImagesButton_Callback in C:\Program Files\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10442)
gui_mainfcn in C:\Program Files\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12182)
CellProfiler in C:\Program Files\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)

I have also attached my pipeline. Any help is appreciated.

PIPEbatch.mat (1.63 KB)


Can you tell me what version of CP 1.0 you are using? You can find this by going to Help > Getting Started, and reporting the number after “CellProfiler version 1.0.XXXX” at the top of the dialog box.


Sorry Mark… it is version 1.0.6025.

In case you are wondering why I am running this version - other people in my department have been analyzing images on our cluster and they recommended that I create the batch files with this version. Of course, they have not run into the problem I described. To set the default image and output folders, I have been manually typing in the addresses. Someone suggested I should map the network drive to the local computer, then use the ‘browse’ function in CellProfiler to select the appropriate folders/paths. Does this sound like it might help? I am going to give it a try tomorrow.

Thanks very much for the help.


That was one of the first things I thought of as well, since you seem to be using an older version of CP. However, it turns out that since you are loading .flex files, there was a bug with handling them in CreateBatchFiles that was subsequently fixed for a later release. So I would recommend upgrading to the latest compiled release or developer’s version of CP 1.0.


Hi Mark,

Thanks for the suggestions. I tried mapping the network drive to the local computer, but I received the same error message. I will try an updated version of CP 1.0 and let you know how it goes.