Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/86887286c60e0ec78f76ef509ef74d/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/6cd187e56139f320649530643b1b45/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/6cd187e56139f320649530643b1b45/.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-ahhsgn58 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 05:07:26,307 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:07:27,606 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:07:27,887 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:07:51,788 - cnv_pipe.batch.run_model - INFO - Loaded data with 68 samples
2026-06-03 05:07:52,083 - cnv_pipe.batch.run_model - INFO - Processing cluster 140 with 158 probes
2026-06-03 05:07:52,714 - cnv_pipe.batch.run_model.cluster140 - INFO - Child process started for cluster 140 with 158 probes
2026-06-03 05:12:06,904 - cnv_pipe.batch.run_model.cluster140 - INFO - Child process finished cluster 140. Wrote cluster_140_samples.csv and cluster_140_params.csv
2026-06-03 05:12:06,906 - cnv_pipe.batch.run_model - INFO - Cluster 140 finished in 254.82 seconds. Status: SUCCESS