Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d3f2ba928beab4f875cf9bd7d52c2c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b91963605f0a32fd1affcb85ba8b98/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b91963605f0a32fd1affcb85ba8b98/.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-z7bs2xa2 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 05:35:14,351 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:35:15,514 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:35:15,734 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:36:08,649 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:36:08,785 - cnv_pipe.batch.run_model - INFO - Processing cluster 1000 with 101 probes
2026-06-03 05:36:09,520 - cnv_pipe.batch.run_model.cluster1000 - INFO - Child process started for cluster 1000 with 101 probes
2026-06-03 05:39:41,374 - cnv_pipe.batch.run_model.cluster1000 - INFO - Child process finished cluster 1000. Wrote cluster_1000_samples.csv and cluster_1000_params.csv
2026-06-03 05:39:41,377 - cnv_pipe.batch.run_model - INFO - Cluster 1000 finished in 212.59 seconds. Status: SUCCESS