Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/5144ad9e68402ab9f76dba7152c49a/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/b3057e1cb477bc4aa38584cb691348/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/b3057e1cb477bc4aa38584cb691348/.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-li6lf23h 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 04:43:14,289 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:43:15,293 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:43:15,491 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:43:32,360 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:43:32,666 - cnv_pipe.batch.run_model - INFO - Processing cluster 923 with 146 probes
2026-06-03 04:43:33,145 - cnv_pipe.batch.run_model.cluster923 - INFO - Child process started for cluster 923 with 146 probes
2026-06-03 04:46:30,088 - cnv_pipe.batch.run_model.cluster923 - INFO - Child process finished cluster 923. Wrote cluster_923_samples.csv and cluster_923_params.csv
2026-06-03 04:46:30,091 - cnv_pipe.batch.run_model - INFO - Cluster 923 finished in 177.42 seconds. Status: SUCCESS