Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/d1e96bfdd243f35cecbdbd35c5ccc5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/02be44bdb567d668b68930eb114a44/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/4a6fee554994dffe5af02adbc2e5c4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/4a6fee554994dffe5af02adbc2e5c4/.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-962l0c8j 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.
2026-06-08 22:24:31,694 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-08 22:24:32,533 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-08 22:24:32,703 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-08 22:24:33,653 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-08 22:24:33,732 - cnv_pipe.batch.run_model - INFO - Processing cluster 1939 with 173 probes
2026-06-08 22:24:34,198 - cnv_pipe.batch.run_model.cluster1939 - INFO - Child process started for cluster 1939 with 173 probes
2026-06-08 22:25:25,356 - cnv_pipe.batch.run_model.cluster1939 - INFO - Child process finished cluster 1939. Wrote cluster_1939_samples.csv and cluster_1939_params.csv
2026-06-08 22:25:25,358 - cnv_pipe.batch.run_model - INFO - Cluster 1939 finished in 51.63 seconds. Status: SUCCESS