Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/7ad2f4ddc4c4a4c48994b5bb742c26/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/7ad2f4ddc4c4a4c48994b5bb742c26/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/c0245ecb359325a9a7b51ebaedf239/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/7ad2f4ddc4c4a4c48994b5bb742c26/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/9b8e65af596a163cd3ee81321f81b6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/9b8e65af596a163cd3ee81321f81b6/.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-g1xuoaxe 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.
2026-05-27 04:56:35,327 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-05-27 04:56:36,151 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-05-27 04:56:36,324 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-05-27 04:56:37,279 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-05-27 04:56:37,463 - cnv_pipe.batch.run_model - INFO - Processing cluster 116 with 181 probes
2026-05-27 04:56:37,872 - cnv_pipe.batch.run_model.cluster116 - INFO - Child process started for cluster 116 with 181 probes
2026-05-27 04:57:33,163 - cnv_pipe.batch.run_model.cluster116 - INFO - Child process finished cluster 116. Wrote cluster_116_samples.csv and cluster_116_params.csv
2026-05-27 04:57:33,164 - cnv_pipe.batch.run_model - INFO - Cluster 116 finished in 55.70 seconds. Status: SUCCESS