Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/8396ef149a740f71c4cc9422d0ea67/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/8396ef149a740f71c4cc9422d0ea67/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/e1a5b8f2f98b00f2a578c316c08f79/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/8396ef149a740f71c4cc9422d0ea67/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/9dd1bcf11ed762d34edab5a2d9a625/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/9dd1bcf11ed762d34edab5a2d9a625/.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-q_v25pad 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 04:59:49,994 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:59:50,947 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:59:51,131 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:00:07,393 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 05:00:07,633 - cnv_pipe.batch.run_model - INFO - Processing cluster 1017 with 199 probes
2026-06-03 05:00:08,084 - cnv_pipe.batch.run_model.cluster1017 - INFO - Child process started for cluster 1017 with 199 probes
2026-06-03 05:03:32,674 - cnv_pipe.batch.run_model.cluster1017 - INFO - Child process finished cluster 1017. Wrote cluster_1017_samples.csv and cluster_1017_params.csv
2026-06-03 05:03:32,676 - cnv_pipe.batch.run_model - INFO - Cluster 1017 finished in 205.04 seconds. Status: SUCCESS