Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/fac372430477ba1f6c897ba5fc7630/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/2bb12c1eefc0e8023c1d2ecf0e8202/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/2bb12c1eefc0e8023c1d2ecf0e8202/.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-nnr9hfg_ 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 05:40:18,443 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:40:19,805 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:40:20,038 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:41:20,365 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:41:20,770 - cnv_pipe.batch.run_model - INFO - Processing cluster 63 with 191 probes
2026-06-03 05:41:21,305 - cnv_pipe.batch.run_model.cluster63 - INFO - Child process started for cluster 63 with 191 probes
2026-06-03 05:47:00,386 - cnv_pipe.batch.run_model.cluster63 - INFO - Child process finished cluster 63. Wrote cluster_63_samples.csv and cluster_63_params.csv
2026-06-03 05:47:00,389 - cnv_pipe.batch.run_model - INFO - Cluster 63 finished in 339.62 seconds. Status: SUCCESS