Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c4911bc2dd2d7bd48f19479b10f175/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c4911bc2dd2d7bd48f19479b10f175/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/75aeaf41b6380bc4dbc477aee55d52/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c4911bc2dd2d7bd48f19479b10f175/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e56168b5da889917eee3a86cf0328a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e56168b5da889917eee3a86cf0328a/.command.run
==> STAGING COMPLETE (6 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-f8q3yzhw because there was an issue with the default path (/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
2026-06-02 19:09:05,569 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 19:09:06,500 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 19:09:06,686 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 19:09:31,696 - cnv_pipe.batch.run_model - INFO - Loaded data with 93 samples
2026-06-02 19:09:31,915 - cnv_pipe.batch.run_model - INFO - Processing cluster 1053 with 88 probes
2026-06-02 19:09:32,333 - cnv_pipe.batch.run_model.cluster1053 - INFO - Child process started for cluster 1053 with 88 probes
2026-06-02 19:11:31,606 - cnv_pipe.batch.run_model.cluster1053 - INFO - Child process finished cluster 1053. Wrote cluster_1053_samples.csv and cluster_1053_params.csv
2026-06-02 19:11:31,607 - cnv_pipe.batch.run_model - INFO - Cluster 1053 finished in 119.69 seconds. Status: SUCCESS