Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/327f035bf8fc6fbcf2fa0d952a6c14/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/5b4805e26a21d69b20f2741d3bddef/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/5b4805e26a21d69b20f2741d3bddef/.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-o29oinvh 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 05:39:06,831 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:39:07,970 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:39:08,183 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:40:00,647 - cnv_pipe.batch.run_model - INFO - Loaded data with 182 samples
2026-06-03 05:40:00,950 - cnv_pipe.batch.run_model - INFO - Processing cluster 999 with 163 probes
2026-06-03 05:40:01,452 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process started for cluster 999 with 163 probes
2026-06-03 05:44:53,087 - 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 05:44:53,090 - cnv_pipe.batch.run_model - INFO - Cluster 999 finished in 292.14 seconds. Status: SUCCESS