Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/9f196e9fa7009d1c77da248079a78c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/a0d974a487a49d22f194645d43f38a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/a0d974a487a49d22f194645d43f38a/.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-3knye7dz 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 05:28:24,154 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:28:25,595 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:28:25,890 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:29:38,416 - cnv_pipe.batch.run_model - INFO - Loaded data with 185 samples
2026-06-03 05:29:38,732 - cnv_pipe.batch.run_model - INFO - Processing cluster 663 with 161 probes
2026-06-03 05:29:39,459 - cnv_pipe.batch.run_model.cluster663 - INFO - Child process started for cluster 663 with 161 probes
2026-06-03 05:36:16,251 - cnv_pipe.batch.run_model.cluster663 - INFO - Child process finished cluster 663. Wrote cluster_663_samples.csv and cluster_663_params.csv
2026-06-03 05:36:16,255 - cnv_pipe.batch.run_model - INFO - Cluster 663 finished in 397.52 seconds. Status: SUCCESS