Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/03d9bd41739068b76caeb84b6843ad/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/03d9bd41739068b76caeb84b6843ad/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/0abbc905604638cc0f1c9bc2c6f05f/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/03d9bd41739068b76caeb84b6843ad/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/d8dbc26d5c5afbd929a6382e248ce9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/d8dbc26d5c5afbd929a6382e248ce9/.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-1ag31fjr 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 05:00:29,782 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:00:30,686 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:00:30,865 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:00:48,297 - cnv_pipe.batch.run_model - INFO - Loaded data with 66 samples
2026-06-03 05:00:48,396 - cnv_pipe.batch.run_model - INFO - Processing cluster 11 with 189 probes
2026-06-03 05:00:49,038 - cnv_pipe.batch.run_model.cluster11 - INFO - Child process started for cluster 11 with 189 probes
2026-06-03 05:03:59,581 - cnv_pipe.batch.run_model.cluster11 - INFO - Child process finished cluster 11. Wrote cluster_11_samples.csv and cluster_11_params.csv
2026-06-03 05:03:59,584 - cnv_pipe.batch.run_model - INFO - Cluster 11 finished in 191.19 seconds. Status: SUCCESS