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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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How long does it take to finish 30X human data? #30

Closed hd00ljy closed 4 years ago

hd00ljy commented 4 years ago

Hi,

I want to know how long does it take to finish methylation calling of 30X 1D human WGS data on 4 Titan V you used.

More specifically I want to know how you get the running time in table S3 of your paper

In table S3, for 30X NA12878 data testing, you wrote that it takes 7366.1min, which corresponds to about 5days.

Does it mean that it takes 5 days even with 4 Titan V GPUs?

Jinyoung

PengNi commented 4 years ago

We used one GPU to test time cost of deepsignal. If using 4 GPUs, it may be 4 times faster.

hd00ljy commented 4 years ago

So it takes ~1 day for 4 GPUs?

PengNi commented 4 years ago

Yes, the deepsignal call_mods step costs ~1 day for 4 GPUs in our experiments.

hd00ljy commented 4 years ago

Thank you!

One last question.

Was the data on the SSD storage or HDD when you measured the time?

I should've organized questions in one post. Sorry for bothering you.

PengNi commented 4 years ago

that's all right. We used HDD storage.

hd00ljy commented 4 years ago

Thank you very much