Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/cbde7a5eb2d873af6c072fe5e4675d/input_2.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/8d780f5496a6ee48021e15a05cf4a1/.command.sh
  Downloading: s3://natera-platform-sandbox/platform_projects/renasight_cnv/renasight_variable_regions.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/8d780f5496a6ee48021e15a05cf4a1/.command.run
  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-kw3gppd6 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 23:11:22,593 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-08 23:11:27,048 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-08 23:11:27,049 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-08 23:11:27,056 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:27,273 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 2883
2026-06-08 23:11:27,481 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 123
2026-06-08 23:11:27,690 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 14
2026-06-08 23:11:27,898 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 3
2026-06-08 23:11:28,109 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 2
2026-06-08 23:11:28,318 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 1
2026-06-08 23:11:28,528 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 0
2026-06-08 23:11:28,739 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-08 23:11:28,739 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-08 23:11:31,488 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-08 23:11:31,488 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-08 23:11:31,496 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:31,708 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 2034
2026-06-08 23:11:31,911 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 65
2026-06-08 23:11:32,115 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 3
2026-06-08 23:11:32,320 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 2
2026-06-08 23:11:32,521 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 1
2026-06-08 23:11:32,723 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 0
2026-06-08 23:11:32,926 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-08 23:11:32,926 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-08 23:11:35,682 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-08 23:11:35,682 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size per probe from covariance of nearby probes, autosomes
2026-06-08 23:11:40,008 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-08 23:11:40,009 - 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_2__sex_calls.png'>
2026-06-08 23:11:51,583 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-08 23:11:51,583 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-08 23:11:51,633 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-08 23:11:51,633 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-08 23:11:51,633 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-08 23:11:51,634 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-08 23:11:51,641 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 304
2026-06-08 23:11:51,649 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 11
2026-06-08 23:11:51,657 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 2
2026-06-08 23:11:51,665 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1
2026-06-08 23:11:51,672 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 0
2026-06-08 23:11:51,681 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 55614
2026-06-08 23:11:51,684 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 0
2026-06-08 23:11:51,687 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-08 23:11:51,688 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY
2026-06-08 23:11:56,951 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-08 23:11:56,951 - 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: 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 23:11:57,037 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-08 23:11:57,037 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-08 23:11:58,985 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-08 23:11:58,985 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-08 23:11:59,340 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-08 23:11:59,340 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-08 23:11:59,346 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete