Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/d656564a34b5914b8cb0e9882f5174/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/d656564a34b5914b8cb0e9882f5174/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/60ff0c8970485a20cfeb406dd9fb72/input_3.csv Downloading: s3://natera-platform-sandbox/platform_projects/renasight_cnv/renasight_variable_regions.bed Downloading: s3://natera-platform-sandbox/platform-users/bding/CNV/REF/Renasight_CNV.mosatic.tm.bed ==> STAGING COMPLETE (5 inputs) mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config' Matplotlib created a temporary cache directory at /tmp/matplotlib-vm26ct4e 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 23:11:22,803 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing 2026-06-08 23:11:27,436 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded 2026-06-08 23:11:27,438 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only. 2026-06-08 23:11:27,444 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 225768 2026-06-08 23:11:27,648 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 1701 2026-06-08 23:11:27,852 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 29 2026-06-08 23:11:28,054 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 2 2026-06-08 23:11:28,255 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 0 2026-06-08 23:11:28,458 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained 2026-06-08 23:11:28,458 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature 2026-06-08 23:11:31,223 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained 2026-06-08 23:11:31,223 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only. 2026-06-08 23:11:31,228 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 225768 2026-06-08 23:11:31,434 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 1385 2026-06-08 23:11:31,634 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 33 2026-06-08 23:11:31,833 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 3 2026-06-08 23:11:32,036 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 0 2026-06-08 23:11:32,243 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts 2026-06-08 23:11:32,243 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks 2026-06-08 23:11:35,026 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks 2026-06-08 23:11:35,026 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size per probe from covariance of nearby probes, autosomes 2026-06-08 23:11:40,258 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained 2026-06-08 23:11:40,258 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get ploidy, all chromosomes /opt/venv/lib/python3.12/site-packages/plotnine/ggplot.py:623: PlotnineWarning: Saving 6 x 5 in image. /opt/venv/lib/python3.12/site-packages/plotnine/ggplot.py:624: PlotnineWarning: Filename: <_io.BufferedWriter name='FC13_cnv_mosaic_3__sex_calls.png'> 2026-06-08 23:11:51,590 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained 2026-06-08 23:11:51,590 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size 2026-06-08 23:11:51,638 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained 2026-06-08 23:11:51,638 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY 2026-06-08 23:11:51,638 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 2026-06-08 23:11:51,639 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0 2026-06-08 23:11:51,646 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 186 2026-06-08 23:11:51,654 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 10 2026-06-08 23:11:51,661 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 7 2026-06-08 23:11:51,669 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 5 2026-06-08 23:11:51,676 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 4 2026-06-08 23:11:51,684 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 3 2026-06-08 23:11:51,692 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 3 2026-06-08 23:11:51,699 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 0 2026-06-08 23:11:51,707 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 55016 2026-06-08 23:11:51,711 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 0 2026-06-08 23:11:51,714 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained 2026-06-08 23:11:51,715 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY 2026-06-08 23:11:59,666 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained 2026-06-08 23:11:59,667 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get the final double norm values, adjusting for ploidies /opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:236: RuntimeWarning: divide by zero encountered in divide /opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:236: RuntimeWarning: invalid value encountered in divide /opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:236: RuntimeWarning: invalid value encountered in divide 2026-06-08 23:11:59,751 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained 2026-06-08 23:11:59,751 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations 2026-06-08 23:12:01,645 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written 2026-06-08 23:12:01,645 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving 2026-06-08 23:12:01,978 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written 2026-06-08 23:12:01,978 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates 2026-06-08 23:12:01,985 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete