Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/c3d8bfb7b4fd5305aa317b2ea43fa9/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/6c3c3e68847b352f2c5500f93c1f81/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/6c3c3e68847b352f2c5500f93c1f81/.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-u153x659 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 04:37:54,756 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:37:56,024 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:37:56,302 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:38:19,864 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:38:19,981 - cnv_pipe.batch.run_model - INFO - Processing cluster 96 with 194 probes
2026-06-03 04:38:20,597 - cnv_pipe.batch.run_model.cluster96 - INFO - Child process started for cluster 96 with 194 probes
2026-06-03 04:43:13,522 - cnv_pipe.batch.run_model.cluster96 - INFO - Child process finished cluster 96. Wrote cluster_96_samples.csv and cluster_96_params.csv
2026-06-03 04:43:13,526 - cnv_pipe.batch.run_model - INFO - Cluster 96 finished in 293.55 seconds. Status: SUCCESS