Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/0beda2781c070bcd33e32f334984f5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/da2e1bcae6d4bf7a6854b6c352e5b5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/da2e1bcae6d4bf7a6854b6c352e5b5/.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-_f98p8rj 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 05:21:51,389 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:21:52,156 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:21:52,321 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:22:42,711 - cnv_pipe.batch.run_model - INFO - Loaded data with 236 samples
2026-06-03 05:22:42,857 - cnv_pipe.batch.run_model - INFO - Processing cluster 87 with 186 probes
2026-06-03 05:22:43,321 - cnv_pipe.batch.run_model.cluster87 - INFO - Child process started for cluster 87 with 186 probes
2026-06-03 05:27:30,735 - cnv_pipe.batch.run_model.cluster87 - INFO - Child process finished cluster 87. Wrote cluster_87_samples.csv and cluster_87_params.csv
2026-06-03 05:27:30,737 - cnv_pipe.batch.run_model - INFO - Cluster 87 finished in 287.88 seconds. Status: SUCCESS