### STEP 1: Network inference based on GRNBoost2 from CLI[](https://render-temp.githubusercontent.com/view/ipynb?color_mode=auto&commit=37e555c112cc4f55a26ef3f7c232ffe9238ae476&enc_url=68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f61657274736c61622f5343454e494370726f746f636f6c2f333765353535633131326363346635356132366566336637633233326666653932333861653437362f6e6f7465626f6f6b732f5343454e494325323050726f746f636f6c2532302d2532304361736525323073747564792532302d2532304d6f757365253230627261696e253230646174612532307365742e6970796e62&nwo=aertslab%2FSCENICprotocol&path=notebooks%2FSCENIC+Protocol+-+Case+study+-+Mouse+brain+data+set.ipynb&repository_id=173955623&repository_type=Repository#STEP-1:-Network-inference-based-on-GRNBoost2-from-CLI)

For this step the CLI version of SCENIC is used. This step can be deployed on an High Performance Computing system.

*Output:* List of adjacencies between a TF and its targets stored in `ADJACENCIES_FNAME`.

!pyscenic grn {COUNTS_QC_MTX_FNAME} {MM_TFS_FNAME} -o {ADJACENCIES_FNAME} --num_workers 32

2019-06-13 17:32:45,044 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.
2019-06-13 17:33:07,766 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
preparing dask client
parsing input
creating dask graph
32 partitions
computing dask graph
not shutting down client, client was created externally
finished
2019-06-13 18:04:23,356 - pyscenic.cli.pyscenic - INFO - Writing results to file.

教程用了半小时，我用了多久呢？

2021-07-14 13:38:39,865 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2021-07-14 13:39:28,686 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
/home/rstudio/miniconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/node.py:155: UserWarning: Port 8787 is already in use.
Perhaps you already have a cluster running?
Hosting the HTTP server on port 41863 instead
  http_address["port"], self.http_server.port
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
preparing dask client
parsing input
creating dask graph
32 partitions
computing dask graph
not shutting down client, client was created externally
finished
distributed.worker - WARNING - Heartbeat to scheduler failed
distributed.worker - WARNING - Heartbeat to scheduler failed

2021-07-14 14:27:07,318 - pyscenic.cli.pyscenic - INFO - Writing results to file.

我用了50min
两年后重复别人的故事