Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d03b578e25999b1cf8c227a4071696/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/805ae22d7f530ffb3c87dc16a71c00/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/805ae22d7f530ffb3c87dc16a71c00/.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-1e7snj95 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 04:51:44,604 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:51:45,490 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:51:45,678 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:52:09,512 - cnv_pipe.batch.run_model - INFO - Loaded data with 87 samples
2026-06-03 04:52:09,740 - cnv_pipe.batch.run_model - INFO - Processing cluster 1239 with 187 probes
2026-06-03 04:52:10,146 - cnv_pipe.batch.run_model.cluster1239 - INFO - Child process started for cluster 1239 with 187 probes
2026-06-03 04:55:51,853 - cnv_pipe.batch.run_model.cluster1239 - INFO - Child process finished cluster 1239. Wrote cluster_1239_samples.csv and cluster_1239_params.csv
2026-06-03 04:55:51,856 - cnv_pipe.batch.run_model - INFO - Cluster 1239 finished in 222.12 seconds. Status: SUCCESS