Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d03b578e25999b1cf8c227a4071696/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/08e1bc0f2848f850ed9c2098fc5df8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/08e1bc0f2848f850ed9c2098fc5df8/.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-tam46m7t 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 04:47:57,130 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:47:57,982 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:47:58,150 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:48:20,519 - cnv_pipe.batch.run_model - INFO - Loaded data with 87 samples
2026-06-03 04:48:20,748 - cnv_pipe.batch.run_model - INFO - Processing cluster 54 with 199 probes
2026-06-03 04:48:21,139 - cnv_pipe.batch.run_model.cluster54 - INFO - Child process started for cluster 54 with 199 probes
2026-06-03 04:52:02,498 - cnv_pipe.batch.run_model.cluster54 - INFO - Child process finished cluster 54. Wrote cluster_54_samples.csv and cluster_54_params.csv
2026-06-03 04:52:02,501 - cnv_pipe.batch.run_model - INFO - Cluster 54 finished in 221.75 seconds. Status: SUCCESS