Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/0beda2781c070bcd33e32f334984f5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/c3d37d8660ded4f58bd9f8372dd68b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/c3d37d8660ded4f58bd9f8372dd68b/.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-zzg858jo 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.
2026-06-03 05:25:16,623 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:25:17,627 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:25:17,836 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:26:16,031 - cnv_pipe.batch.run_model - INFO - Loaded data with 236 samples
2026-06-03 05:26:16,311 - cnv_pipe.batch.run_model - INFO - Processing cluster 563 with 170 probes
2026-06-03 05:26:16,779 - cnv_pipe.batch.run_model.cluster563 - INFO - Child process started for cluster 563 with 170 probes
2026-06-03 05:32:08,585 - cnv_pipe.batch.run_model.cluster563 - INFO - Child process finished cluster 563. Wrote cluster_563_samples.csv and cluster_563_params.csv
2026-06-03 05:32:08,588 - cnv_pipe.batch.run_model - INFO - Cluster 563 finished in 352.28 seconds. Status: SUCCESS