Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/83a6eb5a9efd76c3cc3115568a186b/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/ab47210af094bc091e66714b8a26e2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/ab47210af094bc091e66714b8a26e2/.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-li7qfx5a 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 06:08:30,480 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:08:31,425 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:08:31,643 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:09:18,312 - cnv_pipe.batch.run_model - INFO - Loaded data with 188 samples
2026-06-03 06:09:18,431 - cnv_pipe.batch.run_model - INFO - Processing cluster 559 with 97 probes
2026-06-03 06:09:18,993 - cnv_pipe.batch.run_model.cluster559 - INFO - Child process started for cluster 559 with 97 probes
2026-06-03 06:12:27,659 - cnv_pipe.batch.run_model.cluster559 - INFO - Child process finished cluster 559. Wrote cluster_559_samples.csv and cluster_559_params.csv
2026-06-03 06:12:27,660 - cnv_pipe.batch.run_model - INFO - Cluster 559 finished in 189.23 seconds. Status: SUCCESS