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/f6/c4911bc2dd2d7bd48f19479b10f175/counts_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/2f/897a13d8e91f3586a95386bacf648d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/897a13d8e91f3586a95386bacf648d/.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-6gfwld_9 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 19:07:48,104 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 19:07:48,918 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 19:07:49,101 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 19:08:11,953 - cnv_pipe.batch.run_model - INFO - Loaded data with 93 samples
2026-06-02 19:08:12,212 - cnv_pipe.batch.run_model - INFO - Processing cluster 664 with 154 probes
2026-06-02 19:08:12,581 - cnv_pipe.batch.run_model.cluster664 - INFO - Child process started for cluster 664 with 154 probes
2026-06-02 19:10:54,488 - cnv_pipe.batch.run_model.cluster664 - INFO - Child process finished cluster 664. Wrote cluster_664_samples.csv and cluster_664_params.csv
2026-06-02 19:10:54,490 - cnv_pipe.batch.run_model - INFO - Cluster 664 finished in 162.28 seconds. Status: SUCCESS