Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/53d08abbe7f3c300c6e5e14d79dc78/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/2e00f82c99642261b19ec47a053ac8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/2e00f82c99642261b19ec47a053ac8/.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-i_ku6xxd 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 05:57:31,033 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:57:31,886 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:57:32,051 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:58:11,970 - cnv_pipe.batch.run_model - INFO - Loaded data with 180 samples
2026-06-03 05:58:12,176 - cnv_pipe.batch.run_model - INFO - Processing cluster 999 with 163 probes
2026-06-03 05:58:12,544 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process started for cluster 999 with 163 probes
2026-06-03 06:01:58,043 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process finished cluster 999. Wrote cluster_999_samples.csv and cluster_999_params.csv
2026-06-03 06:01:58,045 - cnv_pipe.batch.run_model - INFO - Cluster 999 finished in 225.87 seconds. Status: SUCCESS