Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/0736553abd3f1ae6189c25cf0a2077/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ca0faff5de2aa0e9773e5c2bcd5de9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ca0faff5de2aa0e9773e5c2bcd5de9/.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-cv9eq37s 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 05:01:33,415 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:01:34,255 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:01:34,431 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:01:50,259 - cnv_pipe.batch.run_model - INFO - Loaded data with 71 samples
2026-06-03 05:01:50,476 - cnv_pipe.batch.run_model - INFO - Processing cluster 77 with 200 probes
2026-06-03 05:01:50,864 - cnv_pipe.batch.run_model.cluster77 - INFO - Child process started for cluster 77 with 200 probes
2026-06-03 05:05:30,066 - cnv_pipe.batch.run_model.cluster77 - INFO - Child process finished cluster 77. Wrote cluster_77_samples.csv and cluster_77_params.csv
2026-06-03 05:05:30,069 - cnv_pipe.batch.run_model - INFO - Cluster 77 finished in 219.59 seconds. Status: SUCCESS