Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/9f196e9fa7009d1c77da248079a78c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/282bf591217f40232c399b8e57c2e1/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/2fc4803127064cd4b3f4f1b0ac78fd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/2fc4803127064cd4b3f4f1b0ac78fd/.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-pn2exi02 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 05:29:33,475 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:29:34,425 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:29:34,613 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:30:23,630 - cnv_pipe.batch.run_model - INFO - Loaded data with 185 samples
2026-06-03 05:30:23,907 - cnv_pipe.batch.run_model - INFO - Processing cluster 996 with 176 probes
2026-06-03 05:30:24,368 - cnv_pipe.batch.run_model.cluster996 - INFO - Child process started for cluster 996 with 176 probes
2026-06-03 05:35:27,247 - cnv_pipe.batch.run_model.cluster996 - INFO - Child process finished cluster 996. Wrote cluster_996_samples.csv and cluster_996_params.csv
2026-06-03 05:35:27,250 - cnv_pipe.batch.run_model - INFO - Cluster 996 finished in 303.34 seconds. Status: SUCCESS