Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/88d8edf348bc0ec8f61d57bcf6e816/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/88d8edf348bc0ec8f61d57bcf6e816/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/4656d30769f4bb945a265cd5e99aad/HCC1395_BL_probe_sample.parquet
==> STAGING COMPLETE (4 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-vimb01id 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.
2026-06-05 21:17:38,233 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading input file: HCC1395_BL_probe_sample.parquet
2026-06-05 21:17:38,289 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading reference genome FASTA file: Homo_sapiens_assembly38.fasta
2026-06-05 21:17:48,918 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Filtered out 458515 probes with mask flags (mask_probes_low, mask_probes_blacklist)
2026-06-05 21:17:48,918 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes (mask_probes_low or mask_probe_model_failed): 458430
2026-06-05 21:17:48,918 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Remaining probes: 4479
2026-06-05 21:17:48,919 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Single sample — skipping batch FC statistics
2026-06-05 21:17:48,919 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processing 1 samples with 1 threads
2026-06-05 21:19:29,183 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processed HCC1395_BL: 5 deletions, 0 duplications
2026-06-05 21:19:29,183 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - 
Processing complete!
2026-06-05 21:19:29,184 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total samples successfully processed: 1
2026-06-05 21:19:29,184 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of samples failed QC: 0
2026-06-05 21:19:29,184 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of probes failed QC: 458430
2026-06-05 21:19:29,184 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total deletions: 5
2026-06-05 21:19:29,184 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total duplications: 0