Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4ca861025b2f4db6b0601212fbe8b8/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4ca861025b2f4db6b0601212fbe8b8/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/2bc6a550b9b7a6a7c04a8c46d11f24/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4ca861025b2f4db6b0601212fbe8b8/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/ed7aec239316affd11cf005343748e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/ed7aec239316affd11cf005343748e/.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-qxona7cq 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.
2026-06-04 17:12:33,330 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 17:12:34,226 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 17:12:34,408 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 17:12:35,458 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 17:12:35,623 - cnv_pipe.batch.run_model - INFO - Processing cluster 562 with 190 probes
2026-06-04 17:12:35,995 - cnv_pipe.batch.run_model.cluster562 - INFO - Child process started for cluster 562 with 190 probes
2026-06-04 17:13:35,823 - cnv_pipe.batch.run_model.cluster562 - INFO - Child process finished cluster 562. Wrote cluster_562_samples.csv and cluster_562_params.csv
2026-06-04 17:13:35,824 - cnv_pipe.batch.run_model - INFO - Cluster 562 finished in 60.20 seconds. Status: SUCCESS