Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/f9dff405351ae9980859be791ec4fd/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/f9dff405351ae9980859be791ec4fd/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/73bca1ba80c4b143f06a4c975cd378/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/f9dff405351ae9980859be791ec4fd/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/556cff4ca6087a94daed68619768b5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/556cff4ca6087a94daed68619768b5/.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-hkwbmh7w 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.
2026-05-28 00:01:37,457 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-05-28 00:01:38,270 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-05-28 00:01:38,434 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-05-28 00:01:39,288 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-05-28 00:01:39,434 - cnv_pipe.batch.run_model - INFO - Processing cluster 996 with 176 probes
2026-05-28 00:01:39,808 - cnv_pipe.batch.run_model.cluster996 - INFO - Child process started for cluster 996 with 176 probes
2026-05-28 00:02:29,863 - cnv_pipe.batch.run_model.cluster996 - INFO - Child process finished cluster 996. Wrote cluster_996_samples.csv and cluster_996_params.csv
2026-05-28 00:02:29,864 - cnv_pipe.batch.run_model - INFO - Cluster 996 finished in 50.43 seconds. Status: SUCCESS