Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/112b8e5e8f3a61fbf890708d7c7cfc/ploidy_1.parquet
Downloading: s3://natera-platform-sandbox/platform_projects/renasight_cnv/zscore_v1.json
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/e8a85f22edf477b69ad37d460c81d4/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/0a401cc23c89250d388893bd4859f6/FC13_cnv_mosaic_1__probe_sample.parquet
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/318b6d99d402f285c0eaa2b51bc27b/clustered_panel.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/e8a85f22edf477b69ad37d460c81d4/.command.run
Downloading: s3://natera-platform-sandbox/platform_projects/renasight_cnv/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
==> STAGING COMPLETE (7 inputs)
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-zy7tqya0 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.
2026-06-08 23:21:20,030 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading input file: FC13_cnv_mosaic_1__probe_sample.parquet
2026-06-08 23:21:20,157 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading panel annotation file: clustered_panel.csv
2026-06-08 23:21:20,410 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading reference genome FASTA file: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Filtered out 72633 probes with mask flags (mask_probes_low, mask_probes_blacklist, mask_probe_model_failed)
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes with coverage below threshold in >50% of samples (mask_probes_low): 1860
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes whose model fit rejected the supplied beta prior (mask_probe_model_failed): 186
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes written to VCF (union, deduplicated): 22
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Remaining probes: 2055207
2026-06-08 23:21:48,467 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading ploidy sample data file: ploidy_1.parquet
2026-06-08 23:21:48,497 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Loaded ploidy data for 93 samples
2026-06-08 23:21:48,497 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Calculating batch-level FC statistics per probe...
2026-06-08 23:21:48,611 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Calculated FC statistics for 22099 probes
2026-06-08 23:21:48,621 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processing sample ID 471141763_r13
2026-06-08 23:21:48,622 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processing 1 samples with 1 threads
2026-06-08 23:21:49,340 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processed 471141763_r13: 9 deletions, 3 duplications
2026-06-08 23:21:49,345 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Wrote 2 rows to CNV call summary: vcfs/cnv_call_summary.tsv
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Wrote 2 rows to gene summary: vcfs/cnv_gene_summary.tsv
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO -
Processing complete!
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total samples successfully processed: 1
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of samples failed QC: 0
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of probes failed QC: 22
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total deletions: 9
2026-06-08 23:21:49,346 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total duplications: 3