Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/d1e96bfdd243f35cecbdbd35c5ccc5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/65dc02ca15614b080750b5d33f2c64/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/65dc02ca15614b080750b5d33f2c64/.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-oimgza2h 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.
2026-06-08 22:24:37,103 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-08 22:24:37,901 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-08 22:24:38,066 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-08 22:24:38,947 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-08 22:24:39,105 - cnv_pipe.batch.run_model - INFO - Processing cluster 1978 with 163 probes
2026-06-08 22:24:39,477 - cnv_pipe.batch.run_model.cluster1978 - INFO - Child process started for cluster 1978 with 163 probes
2026-06-08 22:25:27,854 - cnv_pipe.batch.run_model.cluster1978 - INFO - Child process finished cluster 1978. Wrote cluster_1978_samples.csv and cluster_1978_params.csv
2026-06-08 22:25:27,855 - cnv_pipe.batch.run_model - INFO - Cluster 1978 finished in 48.75 seconds. Status: SUCCESS