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/a7/6dd1a075ef3b84addf95e21b6a10bd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/6dd1a075ef3b84addf95e21b6a10bd/.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-nctdznet 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 18:40:20,541 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:40:21,396 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:40:21,568 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:40:36,465 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:40:36,716 - cnv_pipe.batch.run_model - INFO - Processing cluster 707 with 171 probes
2026-06-02 18:40:37,133 - cnv_pipe.batch.run_model.cluster707 - INFO - Child process started for cluster 707 with 171 probes
2026-06-02 18:43:53,357 - cnv_pipe.batch.run_model.cluster707 - INFO - Child process finished cluster 707. Wrote cluster_707_samples.csv and cluster_707_params.csv
2026-06-02 18:43:53,360 - cnv_pipe.batch.run_model - INFO - Cluster 707 finished in 196.64 seconds. Status: SUCCESS