Troubleshooting

cptools2 cannot access ImageXpress directory.

Make sure you're on a staging node, cptools2 needs to access datastore to extract metadata from the imagexpress filenames.

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Jobs are running but not producing csv files

Check the logs for those jobs.

If there is an error that images cannot be found, then double check the file paths for your scripts. Also due to a bug, make sure that the destaging job only runs after all the analysis tasks have finished. So use the -hold_jid flag, not the -hold_jid_ad in the destaging script.

If there is a MemoryError near the end of the log, then increase the memory requirements in the submission script. This can be changed with both the -l h_vmem and -pe sharedmem.

If there is no error and just ends abruptly without finishing, then it has likely hit the hard run-time limit. This can be adjusted with the -l h_hrt flag.