Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/4054179d8c2faede8275f03a3b1080/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/30097c19dcf0b392a8f6832c904f93/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/30097c19dcf0b392a8f6832c904f93/.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-_7l8yg0y 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.
2026-06-03 21:49:47,237 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 21:49:48,067 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 21:49:48,293 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 21:49:49,328 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-03 21:49:49,541 - cnv_pipe.batch.run_model - INFO - Processing cluster 999 with 163 probes
2026-06-03 21:49:49,930 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process started for cluster 999 with 163 probes
2026-06-03 21:50:40,198 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process finished cluster 999. Wrote cluster_999_samples.csv and cluster_999_params.csv
2026-06-03 21:50:40,199 - cnv_pipe.batch.run_model - INFO - Cluster 999 finished in 50.66 seconds. Status: SUCCESS