Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/0beda2781c070bcd33e32f334984f5/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/13750259501421c12530357a61ef1f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/13750259501421c12530357a61ef1f/.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-a2w8xzip 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 05:27:29,579 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:27:30,430 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:27:30,596 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:28:23,700 - cnv_pipe.batch.run_model - INFO - Loaded data with 236 samples
2026-06-03 05:28:23,984 - cnv_pipe.batch.run_model - INFO - Processing cluster 939 with 184 probes
2026-06-03 05:28:24,398 - cnv_pipe.batch.run_model.cluster939 - INFO - Child process started for cluster 939 with 184 probes
2026-06-03 05:34:13,975 - cnv_pipe.batch.run_model.cluster939 - INFO - Child process finished cluster 939. Wrote cluster_939_samples.csv and cluster_939_params.csv
2026-06-03 05:34:13,978 - cnv_pipe.batch.run_model - INFO - Cluster 939 finished in 349.99 seconds. Status: SUCCESS