Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d03b578e25999b1cf8c227a4071696/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1a570e80bede87829316c5e6d07b9e/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0292be8a67134c5d2b0c7abd3f9783/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0292be8a67134c5d2b0c7abd3f9783/.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-5hu5hltm 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 04:48:07,257 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:48:08,303 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:48:08,503 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:48:32,504 - cnv_pipe.batch.run_model - INFO - Loaded data with 87 samples
2026-06-03 04:48:32,588 - cnv_pipe.batch.run_model - INFO - Processing cluster 99 with 200 probes
2026-06-03 04:48:33,076 - cnv_pipe.batch.run_model.cluster99 - INFO - Child process started for cluster 99 with 200 probes
2026-06-03 04:52:01,085 - cnv_pipe.batch.run_model.cluster99 - INFO - Child process finished cluster 99. Wrote cluster_99_samples.csv and cluster_99_params.csv
2026-06-03 04:52:01,091 - cnv_pipe.batch.run_model - INFO - Cluster 99 finished in 208.50 seconds. Status: SUCCESS