Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/fac372430477ba1f6c897ba5fc7630/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f7ce3b1f69a62c845b540532576663/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/541df9770ae343add4b69b9f1323fb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/541df9770ae343add4b69b9f1323fb/.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-f2ukteaa 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 05:40:25,044 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:40:26,133 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:40:26,377 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:41:23,977 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:41:24,300 - cnv_pipe.batch.run_model - INFO - Processing cluster 88 with 157 probes
2026-06-03 05:41:24,822 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process started for cluster 88 with 157 probes
2026-06-03 05:46:28,894 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process finished cluster 88. Wrote cluster_88_samples.csv and cluster_88_params.csv
2026-06-03 05:46:28,896 - cnv_pipe.batch.run_model - INFO - Cluster 88 finished in 304.60 seconds. Status: SUCCESS