Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7b21e6b3d5296dfad38952efcc4e3e/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/422dcddec2d7e43e358e96417f961e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/422dcddec2d7e43e358e96417f961e/.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-wy9yrafg 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.
2026-06-05 14:05:02,746 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-05 14:05:03,601 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-05 14:05:03,774 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-05 14:05:04,777 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-05 14:05:04,950 - cnv_pipe.batch.run_model - INFO - Processing cluster 990 with 200 probes
2026-06-05 14:05:05,345 - cnv_pipe.batch.run_model.cluster990 - INFO - Child process started for cluster 990 with 200 probes
2026-06-05 14:06:07,490 - cnv_pipe.batch.run_model.cluster990 - INFO - Child process finished cluster 990. Wrote cluster_990_samples.csv and cluster_990_params.csv
2026-06-05 14:06:07,492 - cnv_pipe.batch.run_model - INFO - Cluster 990 finished in 62.54 seconds. Status: SUCCESS