Resume checkpoints in w2rap-contigger?

bioinfologics / w2rap-contigger

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

http://bioinfologics.github.io/the-w2rap-contigger/

MIT License

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Resume checkpoints in w2rap-contigger? #40

Closed mht85 closed 5 years ago

mht85 commented 5 years ago

Hi,

I'm running w2rap-contigger on a HPC and have limited walltime for each job. Is it possible to resume from a certain checkpoint during the run so I can perhaps split jobs into several smaller tasks?

Thanks. mht

jonwright99 commented 5 years ago

Hi @mht85, The contigger can be run step-by-step using the parameters --from_step and --to_step so to run step 1 only you would use --from_step 1 --to_step 1. Intermediate files are dumped from the previous step to be used in the next step. Some of the steps are quicker than others with step 6 being the longest. Best, Jon

mht85 commented 5 years ago

Cool, good to know. I'll give it a try!