Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/85b140281e9b2950cd842c897b7042/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/1baa1eeb10a9d806378d6fd282a9fe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/1baa1eeb10a9d806378d6fd282a9fe/.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-260wtf3y 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 18:35:43,845 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:35:44,656 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:35:44,826 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:35:59,912 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:36:00,136 - cnv_pipe.batch.run_model - INFO - Processing cluster 100 with 178 probes
2026-06-02 18:36:00,542 - cnv_pipe.batch.run_model.cluster100 - INFO - Child process started for cluster 100 with 178 probes
2026-06-02 18:39:25,011 - cnv_pipe.batch.run_model.cluster100 - INFO - Child process finished cluster 100. Wrote cluster_100_samples.csv and cluster_100_params.csv
2026-06-02 18:39:25,014 - cnv_pipe.batch.run_model - INFO - Cluster 100 finished in 204.88 seconds. Status: SUCCESS