Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/a494e8e980c0e7d8e3b4d352c11387/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c3ea7d1398eb3e19fc73c876e222bd/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/3db469a57e6cc33e808aebdda20308/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/3db469a57e6cc33e808aebdda20308/.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-c2l4smhn 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.
2026-06-02 18:38:19,059 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-02 18:38:19,873 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-02 18:38:20,049 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-02 18:38:36,372 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-02 18:38:36,465 - cnv_pipe.batch.run_model - INFO - Processing cluster 973 with 199 probes
2026-06-02 18:38:37,109 - cnv_pipe.batch.run_model.cluster973 - INFO - Child process started for cluster 973 with 199 probes
2026-06-02 18:42:07,769 - cnv_pipe.batch.run_model.cluster973 - INFO - Child process finished cluster 973. Wrote cluster_973_samples.csv and cluster_973_params.csv
2026-06-02 18:42:07,772 - cnv_pipe.batch.run_model - INFO - Cluster 973 finished in 211.31 seconds. Status: SUCCESS