Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/17f7216d35ef4817d7a38ca9bc10c4/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/17f7216d35ef4817d7a38ca9bc10c4/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/41e5c371c3a62eb95974375831623f/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/17f7216d35ef4817d7a38ca9bc10c4/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/5f55d69d83dd5c0b13a5e1e9073a2f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/5f55d69d83dd5c0b13a5e1e9073a2f/.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-06tg6b8r 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 04:53:08,256 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:53:09,114 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:53:09,296 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:53:25,338 - cnv_pipe.batch.run_model - INFO - Loaded data with 65 samples
2026-06-03 04:53:25,571 - cnv_pipe.batch.run_model - INFO - Processing cluster 998 with 199 probes
2026-06-03 04:53:26,013 - cnv_pipe.batch.run_model.cluster998 - INFO - Child process started for cluster 998 with 199 probes
2026-06-03 04:57:13,661 - cnv_pipe.batch.run_model.cluster998 - INFO - Child process finished cluster 998. Wrote cluster_998_samples.csv and cluster_998_params.csv
2026-06-03 04:57:13,664 - cnv_pipe.batch.run_model - INFO - Cluster 998 finished in 228.09 seconds. Status: SUCCESS