I am running CP 2.1 on our computing cluster and for the most part I am having no problems. However, I have one set of images which are giving me an error (these images have 32 series per image rather than \8).
I can create the batch file without any problem. When I go to run the batch file, the first set works absolutely fine.
However, any sets starting after the first gives an error which appears to be related to its ability to find the path of the file (I seem to get the ilastik error even when it runs correctly).
Version: 2014-06-13T13:02:53 22.214.171.1245 / 20140613130253 Plugin directory doesn't point to valid folder: /home/fraserlab/adrian/RunCP/plugins ilastik import: failed to import the ilastik. Please follow the instructions on "http://www.ilastik.org" to install ilastik Traceback (most recent call last): File "/usr/cellprofiler/src/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 81, in <module> import ilastik_main ImportError: No module named ilastik_main Times reported are CPU times for each module, not wall-clock time Error detected during run of module LoadImages Traceback (most recent call last): File "/usr/cellprofiler/src/CellProfiler/cellprofiler/pipeline.py", line 1787, in run_with_yield module.run(workspace) File "/usr/cellprofiler/src/CellProfiler/cellprofiler/modules/loadimages.py", line 2143, in run full_name = url2pathname(url.encode('utf-8')) AttributeError: 'NoneType' object has no attribute 'encode' Mon Jun 16 11:20:50 2014: Image # 97, module LoadImages # 1: 0.00 sec stopping worker thread 0 stopping worker thread 1 stopping worker thread 2 stopping worker thread 3 stopping worker thread 4 stopping worker thread 5 stopping worker thread 6 stopping worker thread 7 stopping worker thread 8 Exiting the JVM monitor thread