Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/20980a8b72434b119805e31e18f186/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/20980a8b72434b119805e31e18f186/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/3300bc457771f74b01342f0d89c948/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/20980a8b72434b119805e31e18f186/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/c8a964409ba3dc81c7fedcd4e4d6f5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/c8a964409ba3dc81c7fedcd4e4d6f5/.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-n6wtjums 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.
2026-05-27 18:54:43,512 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-05-27 18:54:44,326 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-05-27 18:54:44,500 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-05-27 18:54:45,468 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-05-27 18:54:45,664 - cnv_pipe.batch.run_model - INFO - Processing cluster 999 with 163 probes
2026-05-27 18:54:46,056 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process started for cluster 999 with 163 probes
2026-05-27 18:55:35,496 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process finished cluster 999. Wrote cluster_999_samples.csv and cluster_999_params.csv
2026-05-27 18:55:35,497 - cnv_pipe.batch.run_model - INFO - Cluster 999 finished in 49.83 seconds. Status: SUCCESS