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/8d/7859f67ac7c8f5ce0bfe4f7fce4776/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/7859f67ac7c8f5ce0bfe4f7fce4776/.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-56gy3k1b 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 05:33:46,913 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:33:47,986 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:33:48,186 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:34:40,278 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:34:40,398 - cnv_pipe.batch.run_model - INFO - Processing cluster 656 with 97 probes
2026-06-03 05:34:41,155 - cnv_pipe.batch.run_model.cluster656 - INFO - Child process started for cluster 656 with 97 probes
2026-06-03 05:38:13,497 - cnv_pipe.batch.run_model.cluster656 - INFO - Child process finished cluster 656. Wrote cluster_656_samples.csv and cluster_656_params.csv
2026-06-03 05:38:13,499 - cnv_pipe.batch.run_model - INFO - Cluster 656 finished in 213.10 seconds. Status: SUCCESS