Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/83a6eb5a9efd76c3cc3115568a186b/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/3bcabcc434324a5fa1367071f88243/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/3bcabcc434324a5fa1367071f88243/.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-mwywiti5 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 06:05:59,799 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:06:01,318 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:06:01,635 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:07:12,738 - cnv_pipe.batch.run_model - INFO - Loaded data with 188 samples
2026-06-03 06:07:13,086 - cnv_pipe.batch.run_model - INFO - Processing cluster 88 with 157 probes
2026-06-03 06:07:13,885 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process started for cluster 88 with 157 probes
2026-06-03 06:13:20,439 - cnv_pipe.batch.run_model.cluster88 - INFO - Child process finished cluster 88. Wrote cluster_88_samples.csv and cluster_88_params.csv
2026-06-03 06:13:20,441 - cnv_pipe.batch.run_model - INFO - Cluster 88 finished in 367.35 seconds. Status: SUCCESS