Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/c3d8bfb7b4fd5305aa317b2ea43fa9/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/2a3d505911913420c61ebb3510e373/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/2a3d505911913420c61ebb3510e373/.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-9puteb9h 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 04:41:06,108 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:41:06,927 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:41:07,097 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:41:22,257 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:41:22,488 - cnv_pipe.batch.run_model - INFO - Processing cluster 978 with 196 probes
2026-06-03 04:41:22,908 - cnv_pipe.batch.run_model.cluster978 - INFO - Child process started for cluster 978 with 196 probes
2026-06-03 04:44:45,541 - cnv_pipe.batch.run_model.cluster978 - INFO - Child process finished cluster 978. Wrote cluster_978_samples.csv and cluster_978_params.csv
2026-06-03 04:44:45,544 - cnv_pipe.batch.run_model - INFO - Cluster 978 finished in 203.06 seconds. Status: SUCCESS