hal2assemblyhub.py: A Toil workflow can only be started once. Use Toil.restart() to resume it.

[twooldridge]

Hello,

I'm currently running hal2assemblyhub.py using toil & slurm, and there appears to be an error restarting the process. It looked like some jobs failed, and in trying to investigate them by restarting hal2assemblyhub.py by adding the --restart flag, I received the following message:

Traceback (most recent call last):
  File "/private/groups/cgl/cactus/cactus-bin-v2.9.3/bin/hal2assemblyHub.py", line 451, in <module>
    main()
  File "/private/groups/cgl/cactus/cactus-bin-v2.9.3/bin/hal2assemblyHub.py", line 448, in main
    toil.start(Setup(options.halfile, options.outputDirectory, options))
  File "/private/groups/cgl/cactus/cactus-bin-v2.9.3/venv-cactus-v2.9.3/lib/python3.10/site-packages/toil/common.py", line 906, in start
    raise ToilRestartException('A Toil workflow can only be started once. Use '
toil.common.ToilRestartException: A Toil workflow can only be started once. Use Toil.restart() to resume it.

After some brief searching, it seems that this might be because hal2assemblyhub.py is not configured to restart this way? Any suggestions for a work around? Thank you!

Best,
Brock

[glennhickey]

Yeah, this looks like it may be a bug. For context, hal2assemblyHub.py is a very old script that predates toil. But unlike Cactus it hasn't been as well maintained. That said, it's usually pretty quick to run so your best bet is just to rerun from scratch.