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/bd/449e1e7e1f29139c706d42d96783fe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/449e1e7e1f29139c706d42d96783fe/.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-xtzssqo9 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 17:14:41,210 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 17:14:42,002 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 17:14:42,170 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 17:14:43,081 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 17:14:43,158 - cnv_pipe.batch.run_model - INFO - Processing cluster 1200 with 199 probes
2026-06-04 17:14:43,628 - cnv_pipe.batch.run_model.cluster1200 - INFO - Child process started for cluster 1200 with 199 probes
2026-06-04 17:15:40,306 - cnv_pipe.batch.run_model.cluster1200 - INFO - Child process finished cluster 1200. Wrote cluster_1200_samples.csv and cluster_1200_params.csv
2026-06-04 17:15:40,307 - cnv_pipe.batch.run_model - INFO - Cluster 1200 finished in 57.15 seconds. Status: SUCCESS