Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d3f2ba928beab4f875cf9bd7d52c2c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/5ac48a25e592e2ca9f662cc5e1012a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/5ac48a25e592e2ca9f662cc5e1012a/.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-amr3kuha 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 05:35:32,052 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:35:33,271 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:35:33,483 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:36:27,691 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:36:28,052 - cnv_pipe.batch.run_model - INFO - Processing cluster 1003 with 198 probes
2026-06-03 05:36:28,570 - cnv_pipe.batch.run_model.cluster1003 - INFO - Child process started for cluster 1003 with 198 probes
2026-06-03 05:42:20,393 - cnv_pipe.batch.run_model.cluster1003 - INFO - Child process finished cluster 1003. Wrote cluster_1003_samples.csv and cluster_1003_params.csv
2026-06-03 05:42:20,396 - cnv_pipe.batch.run_model - INFO - Cluster 1003 finished in 352.34 seconds. Status: SUCCESS