Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/85b140281e9b2950cd842c897b7042/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/16ca93b053ab3628b5d418852df010/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0e2b84e8b5090761e1000a61f4740b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0e2b84e8b5090761e1000a61f4740b/.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-svv92upn 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.
2026-06-02 18:37:25,837 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:37:26,628 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:37:26,796 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:37:41,867 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:37:41,951 - cnv_pipe.batch.run_model - INFO - Processing cluster 998 with 199 probes
2026-06-02 18:37:42,331 - cnv_pipe.batch.run_model.cluster998 - INFO - Child process started for cluster 998 with 199 probes
2026-06-02 18:41:15,285 - cnv_pipe.batch.run_model.cluster998 - INFO - Child process finished cluster 998. Wrote cluster_998_samples.csv and cluster_998_params.csv
2026-06-02 18:41:15,287 - cnv_pipe.batch.run_model - INFO - Cluster 998 finished in 213.34 seconds. Status: SUCCESS