Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/c6f1a4c7809881b67eefc20778f6dd/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/bbcb4ea34b3015ceeb036609088e25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/bbcb4ea34b3015ceeb036609088e25/.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-fpfu435h 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 21:03:12,966 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 21:03:13,911 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 21:03:14,105 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 21:03:15,142 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-03 21:03:15,217 - cnv_pipe.batch.run_model - INFO - Processing cluster 1000 with 101 probes
2026-06-03 21:03:15,747 - cnv_pipe.batch.run_model.cluster1000 - INFO - Child process started for cluster 1000 with 101 probes
2026-06-03 21:03:52,544 - cnv_pipe.batch.run_model.cluster1000 - INFO - Child process finished cluster 1000. Wrote cluster_1000_samples.csv and cluster_1000_params.csv
2026-06-03 21:03:52,545 - cnv_pipe.batch.run_model - INFO - Cluster 1000 finished in 37.33 seconds. Status: SUCCESS