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/0c/5e53b836da483e097ba8bdb123daf0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/5e53b836da483e097ba8bdb123daf0/.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-2nyaf8b5 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 18:38:58,508 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:38:59,304 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:38:59,479 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:39:15,055 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:39:15,135 - cnv_pipe.batch.run_model - INFO - Processing cluster 700 with 191 probes
2026-06-02 18:39:15,516 - cnv_pipe.batch.run_model.cluster700 - INFO - Child process started for cluster 700 with 191 probes
2026-06-02 18:42:37,164 - cnv_pipe.batch.run_model.cluster700 - INFO - Child process finished cluster 700. Wrote cluster_700_samples.csv and cluster_700_params.csv
2026-06-02 18:42:37,168 - cnv_pipe.batch.run_model - INFO - Cluster 700 finished in 202.03 seconds. Status: SUCCESS