Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/a494e8e980c0e7d8e3b4d352c11387/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/092cce4b633d64098600ab4ad8e601/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/092cce4b633d64098600ab4ad8e601/.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-yknoe2md 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 18:38:51,861 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:38:53,049 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:38:53,297 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:39:15,038 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:39:15,434 - cnv_pipe.batch.run_model - INFO - Processing cluster 1216 with 199 probes
2026-06-02 18:39:15,975 - cnv_pipe.batch.run_model.cluster1216 - INFO - Child process started for cluster 1216 with 199 probes
2026-06-02 18:43:01,199 - cnv_pipe.batch.run_model.cluster1216 - INFO - Child process finished cluster 1216. Wrote cluster_1216_samples.csv and cluster_1216_params.csv
2026-06-02 18:43:01,202 - cnv_pipe.batch.run_model - INFO - Cluster 1216 finished in 225.77 seconds. Status: SUCCESS