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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
27 stars 7 forks source link

Re-run from breaking point #15

Closed liu-xingliang closed 5 years ago

liu-xingliang commented 5 years ago

Hi @yyx8671 ,

I tried to construct denovo assembly on some human dataset. With 128Gb memory and 16 CPUs, the pipline started up six days ago, and it just failed on refineB1 stage complaining in-adequate number of cpus today.

I don't want to re-run the whole pipline again as we are rushing for a deadline. Is there any way that I can re-run the pipline (Pipeline.py) from the breaking point? Thank you very much!

bless~ Xingliang

liu-xingliang commented 5 years ago

Hi @yyx8671 ,

I've tried to use -B parameter in Pipeline.py (need to remove -w in my case), hope that works well.

bless~ Xingliang

liu-xingliang commented 5 years ago

Hi @yyx8671

The pipeline was done using -T 32 -j 20 -L 128 with ~3 weeks. With the help of -B of Pipeline.py, I managed to re-start from step 6: refineB0.

bless~ Xingliang