Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/327f035bf8fc6fbcf2fa0d952a6c14/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/87e87d5b3d392de0309630783bc5dc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/87e87d5b3d392de0309630783bc5dc/.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-5ckvv6kl 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 05:38:19,787 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:38:20,958 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:38:21,167 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:39:15,972 - cnv_pipe.batch.run_model - INFO - Loaded data with 182 samples
2026-06-03 05:39:16,330 - cnv_pipe.batch.run_model - INFO - Processing cluster 686 with 196 probes
2026-06-03 05:39:16,848 - cnv_pipe.batch.run_model.cluster686 - INFO - Child process started for cluster 686 with 196 probes
2026-06-03 05:45:00,258 - cnv_pipe.batch.run_model.cluster686 - INFO - Child process finished cluster 686. Wrote cluster_686_samples.csv and cluster_686_params.csv
2026-06-03 05:45:00,262 - cnv_pipe.batch.run_model - INFO - Cluster 686 finished in 343.93 seconds. Status: SUCCESS