Closed kimh11 closed 3 years ago
Hi HJ,
Paleomix works like make
and should only (re-)run a step in two situations:
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by the pipeline, where the first column represents the status of each file, one of "Ready", "Missing" (1), or "Outdated" (2). If something is going wrong, then you should see already created output files listed as "Outdated" or even as "Missing".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
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 Some of my files had become outdated because I had updated the time on the files to avoid them being scratched.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
Hi Mikkel,
Thanks for a great pipeline! I've conda installed paleomix on a cluster and running the bam pipeline. Sometimes when my run is interrupted, it starts from where it ended, but sometimes it re-run commands that finished and I'm not sure why.
Could you point me to information on how checkpointing on paleomix bam pipeline works?
Thank you!