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dynverse / dynwrap

A common data format and inference environment for single-cell trajectories 📦
https://dynverse.org
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memory issues #157

Open skim245 opened 4 years ago

skim245 commented 4 years ago

I'm trying to run ti_paga and getting memory issues as below

model = dynwrap::infer_trajectory(dataset, ti_paga(), verbose = TRUE) Executing 'paga' on '20200507_013618__data_wrapperwvr0AOl9GO' With parameters: list(filter_features = TRUE, n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L, embedding_type = "fa", connectivity_cutoff = 0.05) inputs: counts priors : start_id Input saved to /tmp/folders/g0/w9p16d056l1d15r38h9r2y8m0000gn/T//RtmpCfNfyx/file84bf5218c660/ti Running method using babelwhale Running /usr/local/bin/docker run --name \ 20200507_025418container__QQk5pCSMeC -e 'TMPDIR=/tmp2' --workdir \ /ti/workspace -v \ '/tmp/folders/g0/w9p16d056l1d15r38h9r2y8m0000gn/T//RtmpCfNfyx/file84bf5218c660/ti:/ti' \ -v \ '/tmp/folders/g0/w9p16d056l1d15r38h9r2y8m0000gn/T//RtmpCfNfyx/file84bf5887f2bb/tmp:/tmp2' \ 'dynverse/ti_paga:v0.9.9.05' --dataset /ti/input.h5 --output \ /ti/output.h5 --use_priors all Container was killed, possibly because it ran out of memory (error code 137)Error: Error during trajectory inference, see output above ↑↑↑

wfma commented 3 years ago

you may want to adjust the docker container memory limit!