Hi CP team,
We’ve been running cellprofiler_v3.1.3 on our computing cluster for a few years without any issues. IT have just installed cellprofiler_v4.0.4 for us, but when I try to submit the jobs to the cluster I’m getting the following error:
File “/config/binaries/miniconda3/4.8.3/envs/cellprofiler_v4.0.4/lib/python3.8/site-packages/cellprofiler_core/image/abstract_image/file/_file_image.py”, line 159, in cache_file
OSError: Test for access to directory failed. Directory: ///W:/CS_DATA_SHARE_03/2020Oct26/A50363_201029120001
Fri Nov 27 08:41:00 2020: Image # 1, module NamesAndTypes # 3: CPU_time = 0.55 secs, Wall_time = 0.49 secs
Something seems to be going wrong when the Batch_data.h5 is created because CellProfiler is looking for the images in the local root path rather than in the cluster root path. I’m using the exact same setup that we’ve always used for v3. Any idea what could be happening? I’ll attach the pipeline and a copy of the sbatch script and output log files.