mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-bwwonhp5 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 23:11:22,430 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-08 23:11:27,090 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-08 23:11:27,092 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-08 23:11:27,099 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:27,312 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 2694
2026-06-08 23:11:27,522 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 106
2026-06-08 23:11:27,729 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 8
2026-06-08 23:11:27,946 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1
2026-06-08 23:11:28,165 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 0
2026-06-08 23:11:28,374 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-08 23:11:28,374 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-08 23:11:31,168 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-08 23:11:31,168 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-08 23:11:31,177 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 228222
2026-06-08 23:11:31,420 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 1615
2026-06-08 23:11:31,628 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 28
2026-06-08 23:11:31,835 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 6
2026-06-08 23:11:32,040 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 0
2026-06-08 23:11:32,252 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-08 23:11:32,252 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-08 23:11:35,064 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-08 23:11:35,064 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size per probe from covariance of nearby probes, autosomes
2026-06-08 23:11:40,315 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-08 23:11:40,315 - 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_4__sex_calls.png'>
2026-06-08 23:11:51,699 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-08 23:11:51,699 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-08 23:11:51,746 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-08 23:11:51,746 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-08 23:11:51,746 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-08 23:11:51,747 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-08 23:11:51,755 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 270
2026-06-08 23:11:51,762 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 12
2026-06-08 23:11:51,770 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 5
2026-06-08 23:11:51,777 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 0
2026-06-08 23:11:51,786 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 55614
2026-06-08 23:11:51,789 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 0
2026-06-08 23:11:51,792 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-08 23:11:51,792 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY
2026-06-08 23:12:01,570 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-08 23:12:01,570 - 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 23:12:01,655 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-08 23:12:01,655 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-08 23:12:03,607 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-08 23:12:03,607 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-08 23:12:03,955 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-08 23:12:03,955 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-08 23:12:03,962 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete