Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/4054179d8c2faede8275f03a3b1080/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ed3093e513c1d37d1ee29fa062c24a/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/727640fa7fdd1c76987a69d4cc5f8a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/727640fa7fdd1c76987a69d4cc5f8a/.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-s2jds3g4 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 21:48:44,382 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 21:48:45,185 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 21:48:45,360 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 21:48:46,400 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-03 21:48:46,472 - cnv_pipe.batch.run_model - INFO - Processing cluster 678 with 188 probes
2026-06-03 21:48:46,852 - cnv_pipe.batch.run_model.cluster678 - INFO - Child process started for cluster 678 with 188 probes
2026-06-03 21:49:42,145 - cnv_pipe.batch.run_model.cluster678 - INFO - Child process finished cluster 678. Wrote cluster_678_samples.csv and cluster_678_params.csv
2026-06-03 21:49:42,147 - cnv_pipe.batch.run_model - INFO - Cluster 678 finished in 55.67 seconds. Status: SUCCESS