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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
424 stars 179 forks source link

pyscenic aucell command does not complete #510

Open leeanapeters opened 11 months ago

leeanapeters commented 11 months ago

Hi, thank you for the great tool!

I have managed to run the inital steps of the workflow but am not able to run aucell as the job is killed regardless of if it is through the command line ( with a range of --num_workers), a slurm script, or in a jupyter notebook.

There is no error other than "killed" output so I am not sure how to troubleshoot. Any help would be appreciated!

Command run:

pyscenic aucell pln_pbmc_filtered_scenic.loom reg.csv --output pyscenic_output_1.loom --num_workers 2

Error encountered: Killed

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file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1694728214446/work jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1649936611996/work jupyterlab_server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server-split_1694531968623/work KDEpy==1.0.10 keras==2.9.0 Keras-Preprocessing==1.1.2 kiwisolver==1.4.5 lark==1.1.2 lazy_loader==0.1rc2 leidenalg==0.8.10 libclang==14.0.1 littleutils==0.2.2 llvmlite==0.41.0 locket==1.0.0 loompy==3.0.7 lz4==4.3.2 Markdown==3.4.2 MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1695367437975/work matplotlib==3.6.3 matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1660814786464/work MiniSom==2.3.0 mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1692116650819/work mongoengine==0.20.0 mpldatacursor==0.7.1 msgpack==1.0.5 multidict==6.0.4 multimethod==1.8 multipledispatch==0.6.0 multiprocessing-on-dill==3.5.0a4 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ghuls commented 8 months ago

Are you sure that you are not just running out of job time on your HPC cluster?