Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d3f2ba928beab4f875cf9bd7d52c2c/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c5e205faa85e96f3060e831bbde3eb/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/ef49ce8ed59f7f98d4f34465730590/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/ef49ce8ed59f7f98d4f34465730590/.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-3vsygncm 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 05:35:19,873 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:35:20,684 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:35:20,853 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:36:07,059 - cnv_pipe.batch.run_model - INFO - Loaded data with 187 samples
2026-06-03 05:36:07,322 - cnv_pipe.batch.run_model - INFO - Processing cluster 960 with 172 probes
2026-06-03 05:36:07,755 - cnv_pipe.batch.run_model.cluster960 - INFO - Child process started for cluster 960 with 172 probes
2026-06-03 05:41:33,540 - cnv_pipe.batch.run_model.cluster960 - INFO - Child process finished cluster 960. Wrote cluster_960_samples.csv and cluster_960_params.csv
2026-06-03 05:41:33,544 - cnv_pipe.batch.run_model - INFO - Cluster 960 finished in 326.22 seconds. Status: SUCCESS