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blachlylab / mucor3

Parses VCF data into tabular spreadsheets and aggregates data by sample
MIT License
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Speed up depthgauge #13

Open Kekananen opened 2 years ago

Kekananen commented 2 years ago

Is there a way to increase the speed of depthgauge besides setting / increasing threads? When running on ~100 viral samples it takes around a day and a half to complete and seems to run more slowly when the number of samples is increased. In the beginning, it quickly works through the first 50 or so, but then slows to an approximate rate of 1 per ~40mins towards the end of processing the samples.

With having threads set to 4, on ~190 samples it took >3 days to finish running. So the average time expected for calculating the depth of viral samples is around ~40mins per sample.

jblachly commented 2 years ago

probably the python code is very inefficient; should never take that long

jblachly commented 2 years ago

It should take like an hour at most