Workers not finding files on s3 when attempting distributed-cellprofiler


#21

just looking at that… my csv file looks like this:

I just tried deleting the PathName cols but that was no good. should they be empty?


#22

No, CP definitely needs the PathName cols to tell it the path to your images, so don’t delete them- I’ve got to head out for the evening, but if you could post the csv, the pipeline, and the job config file that would be helpful in trying to debug it tomorrow!


#23

Yes, I see that, but I can run this pipeline/csv on my laptop with empty PathName cols and proper preferences set in CP gui. I’ll try running the csv with empty cols on aws and send that output if it doesn’t work. the job.json should provide the path to the input. thanks for your help, let’s keep trying! -John


#24

ha! that was it! files are going to my s3 bucket.

<img src="/uploads/cellprofiler/original/2X/6/658f5f0a3ce29bbac1975d6f24fe60c2cc9924d7.png" width=“690” height=“26”

l attached the pipeline and csv in case anyone else is following along:
setlist.csv (5.9 KB)
ExampleSBS_03.cppipe (17.0 KB)

now it’s time for cake!