Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/10f591fad64b7bf6fc8f6bd42f2a73/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/10f591fad64b7bf6fc8f6bd42f2a73/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/cd25ceab0480418b3bcf50cf1021e1/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/10f591fad64b7bf6fc8f6bd42f2a73/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/d955a74c5ed2c21d31283d4be373f4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/d955a74c5ed2c21d31283d4be373f4/.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-lo9d9adu 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.
2026-06-04 19:48:48,748 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 19:48:49,948 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 19:48:50,208 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 19:48:51,584 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 19:48:51,784 - cnv_pipe.batch.run_model - INFO - Processing cluster 1200 with 199 probes
2026-06-04 19:48:52,223 - cnv_pipe.batch.run_model.cluster1200 - INFO - Child process started for cluster 1200 with 199 probes
2026-06-04 19:50:14,246 - cnv_pipe.batch.run_model.cluster1200 - INFO - Child process finished cluster 1200. Wrote cluster_1200_samples.csv and cluster_1200_params.csv
2026-06-04 19:50:14,249 - cnv_pipe.batch.run_model - INFO - Cluster 1200 finished in 82.47 seconds. Status: SUCCESS