checkpointing about paleomix HOT 2 CLOSED

Hi HJ,

Paleomix works like make and should only (re-)run a step in two situations:

1. If the files generated by the step do not exist, or
2. If the files generated by a step are older than the input files to that step, i.e. if the input has changed since the step was last run.

What kind of tasks are you seeing re-run?

Next time a run is interrupted, you can try to run the BAM pipeline with the --list-output-files option. That will print a table of all files generated by the pipeline, where the first column represents the status of each file, one of "Ready", "Missing" (1), or "Outdated" (2). If something is going wrong, then you should see already created output files listed as "Outdated" or even as "Missing".

Cheers,
Mikkel

from paleomix.

Hi Mikkel,

Thank you so much! It was the second situation you listed. Some of my files had become outdated because I had updated the time on the files to avoid them being scratched. Totally my fault. All's back to the way it should be! Really appreciate your help!

Best,
HJ

from paleomix.