Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/8ee81d6b6b4fcd312c228fa48d406e/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/38d48711097b32a19172a708f3bfca/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/38d48711097b32a19172a708f3bfca/.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-76rocbkd 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.
2026-06-04 16:56:50,422 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 16:56:51,237 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 16:56:51,406 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 16:56:52,316 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 16:56:52,470 - cnv_pipe.batch.run_model - INFO - Processing cluster 3 with 188 probes
2026-06-04 16:56:52,837 - cnv_pipe.batch.run_model.cluster3 - INFO - Child process started for cluster 3 with 188 probes
2026-06-04 16:57:50,697 - cnv_pipe.batch.run_model.cluster3 - INFO - Child process finished cluster 3. Wrote cluster_3_samples.csv and cluster_3_params.csv
2026-06-04 16:57:50,699 - cnv_pipe.batch.run_model - INFO - Cluster 3 finished in 58.23 seconds. Status: SUCCESS