Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/ff8de5d7320cf16f51e1a038b6c5df/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/dd67ac0ff8e645ff251ef7ba7699b3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/dd67ac0ff8e645ff251ef7ba7699b3/.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-2gjjn4la 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 06:07:07,297 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:07:08,288 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:07:08,464 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:07:56,192 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 06:07:56,288 - cnv_pipe.batch.run_model - INFO - Processing cluster 787 with 175 probes
2026-06-03 06:07:56,838 - cnv_pipe.batch.run_model.cluster787 - INFO - Child process started for cluster 787 with 175 probes
2026-06-03 06:12:50,182 - cnv_pipe.batch.run_model.cluster787 - INFO - Child process finished cluster 787. Wrote cluster_787_samples.csv and cluster_787_params.csv
2026-06-03 06:12:50,185 - cnv_pipe.batch.run_model - INFO - Cluster 787 finished in 293.90 seconds. Status: SUCCESS