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Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Continue with interrupted RepeatMasker run #211

Closed oushujun closed 1 year ago

oushujun commented 1 year ago

Hello Robert,

Hope all is well. Thank you for developing RepeatMasker!

I installed RepeatMasker via conda. I commonly encounter such a scenario: when annotating genomes with RepeatMasker, the execution was interrupted due to various reasons (eg, running out of disk space, out of walltime, program get killed, etc), leaving a folder with intermediate files. Is it possible to make use of this intermediate folder and continue the interrupted run? It will save a great deal of time, and for those HPC with strict walltimes (ie, 24hrs), it makes it possible to annotate huge genomes.

Best, Shujun

rmhubley commented 1 year ago

I'm afraid there isn't checkpointing integrated into the current RepeatMasker. This is something we are prioritizing in our refactoring work.

oushujun commented 1 year ago

Happy to learn that this is in priority. Looking forward to the refactored Repeatmasker!