Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/201e02d515ce74918c8bbb8d6a7fc4/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/bff97a725822f58539da83397845a4/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/201e02d515ce74918c8bbb8d6a7fc4/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/201e02d515ce74918c8bbb8d6a7fc4/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/88d51bd4018439d38df01afa7c5312/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/88d51bd4018439d38df01afa7c5312/.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-ckiznzua 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 05:13:06,797 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:13:07,612 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:13:07,785 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:13:23,125 - cnv_pipe.batch.run_model - INFO - Loaded data with 71 samples
2026-06-03 05:13:23,335 - cnv_pipe.batch.run_model - INFO - Processing cluster 561 with 190 probes
2026-06-03 05:13:23,712 - cnv_pipe.batch.run_model.cluster561 - INFO - Child process started for cluster 561 with 190 probes
2026-06-03 05:16:25,823 - cnv_pipe.batch.run_model.cluster561 - INFO - Child process finished cluster 561. Wrote cluster_561_samples.csv and cluster_561_params.csv
2026-06-03 05:16:25,826 - cnv_pipe.batch.run_model - INFO - Cluster 561 finished in 182.49 seconds. Status: SUCCESS