mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-ssslhutu 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 23:11:22,471 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-08 23:11:26,853 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-08 23:11:26,854 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-08 23:11:26,862 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:27,068 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 4887
2026-06-08 23:11:27,277 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 193
2026-06-08 23:11:27,480 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 12
2026-06-08 23:11:27,688 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1
2026-06-08 23:11:27,891 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 0
2026-06-08 23:11:28,097 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-08 23:11:28,097 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-08 23:11:31,268 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-08 23:11:31,268 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-08 23:11:31,275 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:31,479 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 3283
2026-06-08 23:11:31,680 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 54
2026-06-08 23:11:31,878 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 3
2026-06-08 23:11:32,078 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1
2026-06-08 23:11:32,275 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 1
2026-06-08 23:11:32,473 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 0
2026-06-08 23:11:32,674 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-08 23:11:32,674 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-08 23:11:35,829 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-08 23:11:35,829 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size per probe from covariance of nearby probes, autosomes
2026-06-08 23:11:39,644 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-08 23:11:39,644 - 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_1__sex_calls.png'>
2026-06-08 23:11:51,970 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-08 23:11:51,970 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-08 23:11:52,016 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-08 23:11:52,016 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-08 23:11:52,016 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-08 23:11:52,017 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-08 23:11:52,025 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 773
2026-06-08 23:11:52,032 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 33
2026-06-08 23:11:52,039 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 2
2026-06-08 23:11:52,046 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 0
2026-06-08 23:11:52,054 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 55614
2026-06-08 23:11:52,058 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 0
2026-06-08 23:11:52,061 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-08 23:11:52,061 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY
2026-06-08 23:11:56,915 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-08 23:11:56,915 - 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 23:11:56,997 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-08 23:11:56,997 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-08 23:11:58,928 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-08 23:11:58,929 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-08 23:11:59,263 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-08 23:11:59,263 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-08 23:11:59,270 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete