Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/86887286c60e0ec78f76ef509ef74d/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/e95e24820800609a9e59f8d37221be/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/e95e24820800609a9e59f8d37221be/.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-ayejbc26 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 05:09:37,231 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:09:38,234 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:09:38,428 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:09:56,557 - cnv_pipe.batch.run_model - INFO - Loaded data with 68 samples
2026-06-03 05:09:56,659 - cnv_pipe.batch.run_model - INFO - Processing cluster 999 with 163 probes
2026-06-03 05:09:57,233 - cnv_pipe.batch.run_model.cluster999 - INFO - Child process started for cluster 999 with 163 probes
2026-06-03 05:12:43,499 - 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 05:12:43,502 - cnv_pipe.batch.run_model - INFO - Cluster 999 finished in 166.84 seconds. Status: SUCCESS