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/39/90f3bf6a03a1368ebb520ddf6fc8e5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/90f3bf6a03a1368ebb520ddf6fc8e5/.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-4_9x_nun 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 22:21:07,617 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-08 22:21:08,526 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-08 22:21:08,707 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-08 22:21:09,728 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-08 22:21:09,913 - cnv_pipe.batch.run_model - INFO - Processing cluster 478 with 199 probes
2026-06-08 22:21:10,308 - cnv_pipe.batch.run_model.cluster478 - INFO - Child process started for cluster 478 with 199 probes
2026-06-08 22:22:12,682 - cnv_pipe.batch.run_model.cluster478 - INFO - Child process finished cluster 478. Wrote cluster_478_samples.csv and cluster_478_params.csv
2026-06-08 22:22:12,683 - cnv_pipe.batch.run_model - INFO - Cluster 478 finished in 62.77 seconds. Status: SUCCESS