Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7b21e6b3d5296dfad38952efcc4e3e/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/2a76610d309579f5160531f647088a/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/11c3ed9edea55e710338804e55b4fb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/11c3ed9edea55e710338804e55b4fb/.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-s08nxjja 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.
2026-06-05 14:03:50,986 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-05 14:03:52,298 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-05 14:03:52,583 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-05 14:03:54,309 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-05 14:03:54,428 - cnv_pipe.batch.run_model - INFO - Processing cluster 561 with 190 probes
2026-06-05 14:03:55,186 - cnv_pipe.batch.run_model.cluster561 - INFO - Child process started for cluster 561 with 190 probes
2026-06-05 14:05:27,605 - cnv_pipe.batch.run_model.cluster561 - INFO - Child process finished cluster 561. Wrote cluster_561_samples.csv and cluster_561_params.csv
2026-06-05 14:05:27,607 - cnv_pipe.batch.run_model - INFO - Cluster 561 finished in 93.18 seconds. Status: SUCCESS