Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/ff8de5d7320cf16f51e1a038b6c5df/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/f9f27a09b601f52e05c80c785a44b5/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/c06e99a5cf8156893e627ceb2123ce/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/c06e99a5cf8156893e627ceb2123ce/.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-76s39o03 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 06:07:40,699 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:07:41,569 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:07:41,743 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:08:25,426 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 06:08:25,657 - cnv_pipe.batch.run_model - INFO - Processing cluster 939 with 184 probes
2026-06-03 06:08:26,095 - cnv_pipe.batch.run_model.cluster939 - INFO - Child process started for cluster 939 with 184 probes
2026-06-03 06:13:29,505 - cnv_pipe.batch.run_model.cluster939 - INFO - Child process finished cluster 939. Wrote cluster_939_samples.csv and cluster_939_params.csv
2026-06-03 06:13:29,507 - cnv_pipe.batch.run_model - INFO - Cluster 939 finished in 303.85 seconds. Status: SUCCESS