mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-cvpmngme 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.
2026-06-02 18:22:34,890 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-02 18:23:05,020 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-02 18:23:05,025 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-02 18:23:05,149 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1861536
2026-06-02 18:23:12,674 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 223484
2026-06-02 18:23:20,165 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 13745
2026-06-02 18:23:27,626 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 3496
2026-06-02 18:23:35,134 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1074
2026-06-02 18:23:42,675 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 495
2026-06-02 18:23:50,253 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 155
2026-06-02 18:23:57,830 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 95
2026-06-02 18:24:05,442 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 41
2026-06-02 18:24:12,986 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 14
2026-06-02 18:24:20,543 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 2
2026-06-02 18:24:28,101 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 1
2026-06-02 18:24:35,669 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 0
2026-06-02 18:24:43,196 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-02 18:24:43,196 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-02 18:24:49,668 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-02 18:24:49,668 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-02 18:24:49,799 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1861536
2026-06-02 18:24:59,639 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 222178
2026-06-02 18:25:09,478 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 13760
2026-06-02 18:25:19,331 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 3547
2026-06-02 18:25:29,180 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 1107
2026-06-02 18:25:39,033 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 550
2026-06-02 18:25:48,914 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 193
2026-06-02 18:25:58,797 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 67
2026-06-02 18:26:08,643 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 23
2026-06-02 18:26:18,455 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 10
2026-06-02 18:26:28,347 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 9
2026-06-02 18:26:38,200 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 4
2026-06-02 18:26:48,134 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 1
2026-06-02 18:26:58,137 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 13, outliers: 1
2026-06-02 18:27:08,201 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 14, outliers: 0
2026-06-02 18:27:18,261 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-02 18:27:18,262 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-02 18:28:13,496 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-02 18:28:13,496 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size per probe from covariance of nearby probes, autosomes
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -106.570438101933433). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -106.570438101933433). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -106.570438101933433). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -106.570438101933433). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -106.570438101933433). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.007578329440619 > -105.584608294949447). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.577657364324466 > -93.069811763233503). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.577657364324466 > -93.069811763233503). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.614152140456767 > -93.201429914614181). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.614152140457008 > -95.155903618025718). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.614152140456767 > -93.201429914614181). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.614152140456767 > -93.201429914614181). You may want to try with a higher value of support_fraction (current value: 0.527).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.117467666022289 > -42.524306725844546). You may want to try with a higher value of support_fraction (current value: 0.522).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.117467666022289 > -42.524306725844546). You may want to try with a higher value of support_fraction (current value: 0.522).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.117467666022289 > -42.524306725844546). You may want to try with a higher value of support_fraction (current value: 0.522).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.117467666022289 > -42.524306725844546). You may want to try with a higher value of support_fraction (current value: 0.522).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.454542394567458 > -44.227759883846879). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.499207827483957 > -125.423585029895094). You may want to try with a higher value of support_fraction (current value: 0.550).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-39.572227312956016 > -126.763140547587881). You may want to try with a higher value of support_fraction (current value: 0.550).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-39.572227312956016 > -126.763140547587881). You may want to try with a higher value of support_fraction (current value: 0.550).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-39.572227312956016 > -126.763140547587881). You may want to try with a higher value of support_fraction (current value: 0.550).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-39.572227312956016 > -126.763140547587881). You may want to try with a higher value of support_fraction (current value: 0.550).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-136.795927470385976 > -166.021149878733468). You may want to try with a higher value of support_fraction (current value: 0.654).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-136.795927470385976 > -166.021149878733468). You may want to try with a higher value of support_fraction (current value: 0.654).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-136.795927470385976 > -166.021149878733468). You may want to try with a higher value of support_fraction (current value: 0.654).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-136.795927470385976 > -166.021149878733468). You may want to try with a higher value of support_fraction (current value: 0.654).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-179.112855488418859 > -180.606016552170331). You may want to try with a higher value of support_fraction (current value: 0.593).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-262.237626867662584 > -263.878164771576678). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-206.962155827578727 > -208.124630722498750). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-149.149122755300994 > -149.888265476052226). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-255.661467855181854 > -257.651725357463874). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-225.439853865369003 > -226.150504706683591). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-145.950084430111218 > -146.331881069407416). You may want to try with a higher value of support_fraction (current value: 0.585).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.690587054557483 > -129.457240415061705). You may want to try with a higher value of support_fraction (current value: 0.582).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.063358083047440 > -49.655008330628910). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.063358083047440 > -49.655008330628910). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.063358083047440 > -49.655008330628910). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.063358083047440 > -49.655008330628910). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-219.425638183185185 > -221.595233399101460). You may want to try with a higher value of support_fraction (current value: 0.611).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-219.425638183185185 > -221.595233399101460). You may want to try with a higher value of support_fraction (current value: 0.611).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-258.249778000681829 > -260.103158527635571). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-258.249778000681829 > -260.103158527635571). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.999231578019788 > -108.852749064171121). You may want to try with a higher value of support_fraction (current value: 0.607).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.999231578019788 > -108.852749064171121). You may want to try with a higher value of support_fraction (current value: 0.607).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-120.106320815056904 > -122.278656398692320). You may want to try with a higher value of support_fraction (current value: 0.623).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-222.114122068663562 > -222.490815553879230). You may want to try with a higher value of support_fraction (current value: 0.649).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-222.114122068663562 > -222.490815553879230). You may want to try with a higher value of support_fraction (current value: 0.649).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-142.437429393715291 > -143.482347592215490). You may want to try with a higher value of support_fraction (current value: 0.603).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-140.797417855036826 > -141.512664187720645). You may want to try with a higher value of support_fraction (current value: 0.603).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-140.595855575418767 > -141.143864016069188). You may want to try with a higher value of support_fraction (current value: 0.603).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-62.679176580110678 > -102.892522595684298). You may want to try with a higher value of support_fraction (current value: 0.556).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-120.912358680913755 > -120.977218908252027). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-120.912358680913755 > -121.289399024663282). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-120.912358680913755 > -120.977218908252027). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-120.912358680913755 > -121.289399024663282). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-87.761512969420323 > -114.173108944917374). You may want to try with a higher value of support_fraction (current value: 0.574).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-126.582631786296389 > -126.925128553106077). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-124.508247837251758 > -125.654994165141289). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-124.878210086137841 > -126.885027362558759). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.018606328812538 > -102.990756573938256). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.018606328812538 > -102.990756573938256). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.018606328812538 > -102.990756573938256). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.018606328812538 > -102.990756573938256). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.018606328812538 > -102.990756573938256). You may want to try with a higher value of support_fraction (current value: 0.571).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-41.674034076111212 > -108.589551489963625). You may want to try with a higher value of support_fraction (current value: 0.542).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-146.505278782485192 > -146.574677631663945). You may want to try with a higher value of support_fraction (current value: 0.558).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-65.699884193486824 > -104.487832954452557). You may want to try with a higher value of support_fraction (current value: 0.562).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-109.872574897250544 > -109.956466329161884). You may want to try with a higher value of support_fraction (current value: 0.564).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-109.872574897250544 > -110.107832682036332). You may want to try with a higher value of support_fraction (current value: 0.564).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-110.900731708672339 > -112.565686369339275). You may want to try with a higher value of support_fraction (current value: 0.564).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-140.506907176764798 > -151.518521220818059). You may want to try with a higher value of support_fraction (current value: 0.577).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-113.720804382394888 > -143.862984938996021). You may want to try with a higher value of support_fraction (current value: 0.565).
2026-06-02 18:40:33,882 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-02 18:40:33,883 - 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='A2375WFLT3_1__sex_calls.png'>
2026-06-02 18:41:43,487 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-02 18:41:43,488 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-02 18:41:46,246 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-02 18:41:46,247 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-02 18:41:46,247 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-02 18:41:46,258 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-02 18:41:46,546 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 9215
2026-06-02 18:41:46,834 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 768
2026-06-02 18:41:47,107 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 152
2026-06-02 18:41:47,378 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 21
2026-06-02 18:41:47,601 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 9
2026-06-02 18:41:47,832 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 1
2026-06-02 18:41:48,068 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 0
2026-06-02 18:41:48,321 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-02 18:41:48,325 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 595
2026-06-02 18:41:48,329 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 29
2026-06-02 18:41:48,333 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 15
2026-06-02 18:41:48,338 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 2
2026-06-02 18:41:48,341 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 1
2026-06-02 18:41:48,345 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 0
2026-06-02 18:41:48,351 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-02 18:41:48,351 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.603633563761459 > -49.479921250881759). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.470819539634014 > -49.273119767692116). You may want to try with a higher value of support_fraction (current value: 0.548).
2026-06-02 18:42:24,307 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-02 18:42:24,308 - 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:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
2026-06-02 18:42:26,032 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-02 18:42:26,032 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-02 18:43:00,352 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-02 18:43:00,353 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-02 18:43:03,995 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-02 18:43:03,995 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-02 18:43:04,008 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete