Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/0beda2781c070bcd33e32f334984f5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/bcd65b890b429135e8bcdf98596937/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/bcd65b890b429135e8bcdf98596937/.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-5un0mhgv 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 05:21:53,631 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:21:54,412 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:21:54,584 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:22:43,395 - cnv_pipe.batch.run_model - INFO - Loaded data with 236 samples
2026-06-03 05:22:43,647 - cnv_pipe.batch.run_model - INFO - Processing cluster 99 with 200 probes
2026-06-03 05:22:44,017 - cnv_pipe.batch.run_model.cluster99 - INFO - Child process started for cluster 99 with 200 probes
2026-06-03 05:27:45,862 - cnv_pipe.batch.run_model.cluster99 - INFO - Child process finished cluster 99. Wrote cluster_99_samples.csv and cluster_99_params.csv
2026-06-03 05:27:45,865 - cnv_pipe.batch.run_model - INFO - Cluster 99 finished in 302.22 seconds. Status: SUCCESS