Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/0736553abd3f1ae6189c25cf0a2077/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/487893c6fdbef35040025b83ccc06f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/487893c6fdbef35040025b83ccc06f/.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-llsjud3c 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 05:04:41,201 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:04:41,995 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:04:42,173 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:04:59,169 - cnv_pipe.batch.run_model - INFO - Loaded data with 71 samples
2026-06-03 05:04:59,409 - cnv_pipe.batch.run_model - INFO - Processing cluster 1042 with 186 probes
2026-06-03 05:04:59,787 - cnv_pipe.batch.run_model.cluster1042 - INFO - Child process started for cluster 1042 with 186 probes
2026-06-03 05:08:21,969 - cnv_pipe.batch.run_model.cluster1042 - INFO - Child process finished cluster 1042. Wrote cluster_1042_samples.csv and cluster_1042_params.csv
2026-06-03 05:08:21,973 - cnv_pipe.batch.run_model - INFO - Cluster 1042 finished in 202.56 seconds. Status: SUCCESS