Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/966eb439bad0ff0fba17c0eb35496a/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/966eb439bad0ff0fba17c0eb35496a/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/88572080cac8faab76fdfbecb1c1e0/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/966eb439bad0ff0fba17c0eb35496a/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/22b5e39338652fdc5bb57d6472c0ab/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/22b5e39338652fdc5bb57d6472c0ab/.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-lqlwe7em 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.
2026-06-05 20:53:59,577 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-05 20:54:00,356 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-05 20:54:00,518 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-05 20:54:01,338 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-05 20:54:01,475 - cnv_pipe.batch.run_model - INFO - Processing cluster 88 with 157 probes
2026-06-05 20:54:01,833 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process started for cluster 88 with 157 probes
2026-06-05 20:54:46,874 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process finished cluster 88. Wrote cluster_88_samples.csv and cluster_88_params.csv
2026-06-05 20:54:46,875 - cnv_pipe.batch.run_model - INFO - Cluster 88 finished in 45.40 seconds. Status: SUCCESS