Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/ff8de5d7320cf16f51e1a038b6c5df/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/e610f62223c2b7d359f2f4fcb7d31a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/e610f62223c2b7d359f2f4fcb7d31a/.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-hjembv7d 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 06:05:43,836 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:05:44,767 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:05:44,951 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:06:29,490 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 06:06:29,709 - cnv_pipe.batch.run_model - INFO - Processing cluster 474 with 197 probes
2026-06-03 06:06:30,115 - cnv_pipe.batch.run_model.cluster474 - INFO - Child process started for cluster 474 with 197 probes
2026-06-03 06:11:47,587 - cnv_pipe.batch.run_model.cluster474 - INFO - Child process finished cluster 474. Wrote cluster_474_samples.csv and cluster_474_params.csv
2026-06-03 06:11:47,589 - cnv_pipe.batch.run_model - INFO - Cluster 474 finished in 317.88 seconds. Status: SUCCESS