When running a job that was part of a larger batch file I was presented with a really strange error whereby some of the CP jobs are trying to access parts of the filesystem that are not in any way associated with the input for the batch file. The input selected is everything below the default input folder:
Yet for at least one of these jobs, CP was trying to search for flex files in a completely different part of the filesystem:
Exception in thread "Thread-0" loci.formats.UnknownFormatException: Unknown file format: /home/lee/lipid_droplets/code/.svn/text-base/rename_flex.py.svn-base
ERROR:root:Failed to prepare run for module LoadImages
How CP was trying to search in /home/lee/lipid_droplets/… is beyond me. I’ve attached the full error message as well as the .cp file that was used to generate the batch file for this set of jobs. I really don’t quite know where to start debugging this issue, so any help you can provide is appreciated.