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/cf/d951e501a812c80f2e73e9d924af6f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d951e501a812c80f2e73e9d924af6f/.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-s6fw70ur 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 17:11:04,638 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 17:11:05,475 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 17:11:05,651 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 17:11:06,640 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 17:11:06,816 - cnv_pipe.batch.run_model - INFO - Processing cluster 100 with 178 probes
2026-06-04 17:11:07,202 - cnv_pipe.batch.run_model.cluster100 - INFO - Child process started for cluster 100 with 178 probes
2026-06-04 17:12:02,733 - cnv_pipe.batch.run_model.cluster100 - INFO - Child process finished cluster 100. Wrote cluster_100_samples.csv and cluster_100_params.csv
2026-06-04 17:12:02,734 - cnv_pipe.batch.run_model - INFO - Cluster 100 finished in 55.92 seconds. Status: SUCCESS