Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d3f2ba928beab4f875cf9bd7d52c2c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/a8e776fa26efebb765775801ea0bfc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/a8e776fa26efebb765775801ea0bfc/.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-w37uik3r 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.
2026-06-03 05:35:15,112 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:35:15,922 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:35:16,102 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:35:59,728 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:35:59,988 - cnv_pipe.batch.run_model - INFO - Processing cluster 704 with 156 probes
2026-06-03 05:36:00,401 - cnv_pipe.batch.run_model.cluster704 - INFO - Child process started for cluster 704 with 156 probes
2026-06-03 05:41:11,328 - cnv_pipe.batch.run_model.cluster704 - INFO - Child process finished cluster 704. Wrote cluster_704_samples.csv and cluster_704_params.csv
2026-06-03 05:41:11,331 - cnv_pipe.batch.run_model - INFO - Cluster 704 finished in 311.34 seconds. Status: SUCCESS