mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-4c8u7rke 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.
2026-06-03 04:27:21,917 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-03 04:27:57,790 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-03 04:27:57,798 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-03 04:27:57,939 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1861536
2026-06-03 04:28:07,328 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 631396
2026-06-03 04:28:15,359 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 81375
2026-06-03 04:28:23,597 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 14948
2026-06-03 04:28:31,537 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 3249
2026-06-03 04:28:39,342 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 1080
2026-06-03 04:28:46,946 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 383
2026-06-03 04:28:54,840 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 156
2026-06-03 04:29:02,687 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 89
2026-06-03 04:29:10,438 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 37
2026-06-03 04:29:18,162 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 11
2026-06-03 04:29:25,904 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 6
2026-06-03 04:29:33,699 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 4
2026-06-03 04:29:41,627 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 13, outliers: 0
2026-06-03 04:29:49,304 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-03 04:29:49,305 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-03 04:29:56,098 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-03 04:29:56,099 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-03 04:29:56,241 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1861536
2026-06-03 04:30:09,447 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 602638
2026-06-03 04:30:20,340 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 73753
2026-06-03 04:30:31,391 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 12673
2026-06-03 04:30:42,378 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 2382
2026-06-03 04:30:53,140 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 822
2026-06-03 04:31:03,762 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 375
2026-06-03 04:31:14,318 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 119
2026-06-03 04:31:24,881 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 66
2026-06-03 04:31:35,632 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 21
2026-06-03 04:31:45,947 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 12
2026-06-03 04:31:56,286 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 5
2026-06-03 04:32:07,189 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 4
2026-06-03 04:32:17,910 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 13, outliers: 0
2026-06-03 04:32:28,852 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-03 04:32:28,853 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-03 04:33:24,446 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-03 04:33:24,446 - 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) (-12.515266037830289 > -47.102393664541907). You may want to try with a higher value of support_fraction (current value: 0.517).
/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) (-12.515266037830289 > -47.102393664541907). You may want to try with a higher value of support_fraction (current value: 0.517).
/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) (-12.515266037830289 > -47.102393664541907). You may want to try with a higher value of support_fraction (current value: 0.517).
/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) (-12.515266037830289 > -47.102393664541907). You may want to try with a higher value of support_fraction (current value: 0.517).
/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) (-12.515266037830289 > -47.102393664541907). You may want to try with a higher value of support_fraction (current value: 0.517).
/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) (-52.686743636672325 > -120.272806867726132). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.871921526056418 > -92.366772063523513). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.726308218520650 > -91.709934161100222). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.954839124300833 > -119.391320041057355). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.686743636672325 > -120.272806867726132). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.871921526056418 > -92.366772063523513). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.726308218520650 > -91.709934161100222). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.954839124300833 > -119.391320041057355). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.686743636672325 > -120.272806867726132). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.871921526056418 > -92.366772063523513). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.726308218520650 > -91.709934161100222). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-52.954839124300833 > -119.391320041057355). You may want to try with a higher value of support_fraction (current value: 0.561).
/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) (-5.317884397576520 > -42.462095627315271). You may want to try with a higher value of support_fraction (current value: 0.541).
/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) (-5.317884397576520 > -42.462095627315271). You may want to try with a higher value of support_fraction (current value: 0.541).
/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) (-82.010698523885807 > -116.905426016431704). You may want to try with a higher value of support_fraction (current value: 0.578).
/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) (-85.821397410350187 > -177.320676322489533). You may want to try with a higher value of support_fraction (current value: 0.576).
/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) (-84.447486118458002 > -115.019446778034322). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-87.157822880748711 > -118.832370278272123). You may want to try with a higher value of support_fraction (current value: 0.595).
/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) (-85.922377563435475 > -117.862859658206816). You may want to try with a higher value of support_fraction (current value: 0.595).
/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) (-67.952528380020780 > -101.260323372724855). You may want to try with a higher value of support_fraction (current value: 0.573).
/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) (-67.952528380020780 > -101.260323372724855). You may want to try with a higher value of support_fraction (current value: 0.573).
/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) (-62.134204423136268 > -94.069178256125028). You may want to try with a higher value of support_fraction (current value: 0.573).
/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) (-61.836604013603974 > -93.911464352842813). You may want to try with a higher value of support_fraction (current value: 0.573).
/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) (-60.523878286318286 > -94.726899383531702). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-60.352627886352252 > -125.463891973067163). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-60.275970854015696 > -94.534918532755626). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-60.244731900076012 > -92.648903152933912). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-60.004306992354856 > -92.156469311281811). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-75.964665141200072 > -110.035854162691948). You may want to try with a higher value of support_fraction (current value: 0.576).
/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) (-75.144698245687650 > -110.453557619511074). You may want to try with a higher value of support_fraction (current value: 0.576).
/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) (-74.573487979507988 > -144.167045686554758). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-78.300272500226129 > -170.684411441541101). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-80.470030917160273 > -169.398964562831566). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-80.470030917160273 > -170.959884684766337). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-80.470030917160273 > -169.398964562831566). You may want to try with a higher value of support_fraction (current value: 0.570).
/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) (-106.632964872325942 > -107.822347435295853). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-7.871732119513229 > -43.836892787158547). You may want to try with a higher value of support_fraction (current value: 0.524).
/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) (-7.871732119513229 > -43.836892787158547). You may want to try with a higher value of support_fraction (current value: 0.524).
/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) (-7.871732119513229 > -43.836892787158547). You may want to try with a higher value of support_fraction (current value: 0.524).
/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) (-201.912840773653301 > -251.106428052730166). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-20.559189574892759 > -51.553778121091163). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-5.804533720881089 > -41.132669370545116). You may want to try with a higher value of support_fraction (current value: 0.523).
/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) (-40.621238118348472 > -96.177216561287821). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-40.692544141277835 > -97.746357593856828). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-64.522338955997782 > -96.743050963364979). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-40.621238118348472 > -96.177216561287821). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-40.692544141277835 > -97.746357593856828). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-64.522338955997782 > -96.743050963364979). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-40.621238118348472 > -96.177216561287821). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-40.692544141277835 > -97.746357593856828). You may want to try with a higher value of support_fraction (current value: 0.580).
/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) (-64.522338955997782 > -96.743050963364979). You may want to try with a higher value of support_fraction (current value: 0.580).
2026-06-03 04:34:54,772 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (5) for probe 377368. MinCovDet requires more samples than features.
2026-06-03 04:34:54,773 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (5) for probe 377369. MinCovDet requires more samples than features.
2026-06-03 04:34:54,774 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (5) for probe 377370. MinCovDet requires more samples than features.
2026-06-03 04:34:54,774 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (5) for probe 377371. MinCovDet requires more samples than features.
2026-06-03 04:34:54,774 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (5) for probe 377372. MinCovDet requires more samples than features.
/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) (-108.814263879592332 > -168.867657732864529). You may want to try with a higher value of support_fraction (current value: 0.617).
/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) (-103.994279532277375 > -106.144470975000345). You may want to try with a higher value of support_fraction (current value: 0.592).
/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) (-90.253175210880983 > -90.906326871994295). You may want to try with a higher value of support_fraction (current value: 0.573).
/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) (-111.543230933917172 > -180.238063170533422). You may want to try with a higher value of support_fraction (current value: 0.600).
/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) (-111.543230933917172 > -180.238063170533422). You may want to try with a higher value of support_fraction (current value: 0.600).
/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) (-98.796700867282510 > -166.491496782213545). You may want to try with a higher value of support_fraction (current value: 0.588).
/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) (-98.796700867282510 > -166.491496782213545). You may want to try with a higher value of support_fraction (current value: 0.588).
/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) (-173.223408645928970 > -173.872902886022644). 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) (-170.339475330660406 > -170.647404460899651). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-162.168713452489186 > -163.108921089097890). 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) (-161.926387240756782 > -161.931481773120680). 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) (-176.985282069918753 > -179.009059942437403). You may want to try with a higher value of support_fraction (current value: 0.588).
/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) (-176.985282069918753 > -179.009059942437403). You may want to try with a higher value of support_fraction (current value: 0.588).
/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) (-140.245453288957265 > -140.274389647208494). 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) (-136.958716782504581 > -136.967166496880964). 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) (-144.030170232474774 > -144.925571516208208). 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) (-145.393501774015817 > -147.721182021931980). 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) (-144.016311563654995 > -144.556820694426875). 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) (-139.285004977490473 > -139.291264527155988). 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) (-140.245453288957265 > -140.274389647208494). 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) (-136.958716782504581 > -136.967166496880964). 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) (-144.030170232474774 > -144.925571516208208). 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) (-145.393501774015817 > -147.721182021931980). 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) (-144.016311563654995 > -144.556820694426875). 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) (-139.285004977490473 > -139.291264527155988). 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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-185.778955329535677 > -187.793823464296167). You may want to try with a higher value of support_fraction (current value: 0.618).
/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) (-215.163528936749003 > -216.442902549630077). 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) (-189.025126442054074 > -190.425486777858055). 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) (-154.932886388535252 > -155.349416145401790). 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) (-42.147962374240407 > -104.027482881959429). You may want to try with a higher value of support_fraction (current value: 0.559).
/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) (-42.147962374240407 > -104.027482881959429). You may want to try with a higher value of support_fraction (current value: 0.559).
/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) (-52.869727309719501 > -119.199966113772092). 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) (-53.756457021312784 > -116.327850354500839). 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) (-53.321071437674419 > -117.753485117542539). 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) (-52.869727309719501 > -119.199966113772092). 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) (-53.756457021312784 > -116.327850354500839). 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) (-53.321071437674419 > -117.753485117542539). 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) (-52.869727309719501 > -119.199966113772092). 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) (-53.756457021312784 > -116.327850354500839). 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) (-53.321071437674419 > -117.753485117542539). 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) (-55.098349945362393 > -118.467134133414845). 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) (-55.371803383875260 > -119.615119716062196). 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) (-59.784333267843927 > -127.021702179556556). You may want to try with a higher value of support_fraction (current value: 0.568).
/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) (-50.288480078070009 > -130.887827738625845). 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) (-50.288480078070009 > -130.887827738625845). 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) (-50.288480078070009 > -130.887827738625845). 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) (-50.288480078070009 > -130.887827738625845). 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) (-141.564600179856654 > -142.600225857038538). You may want to try with a higher value of support_fraction (current value: 0.575).
/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: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) (-164.519269346711297 > -170.064446791196929). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-151.421802236177029 > -156.501289763388172). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-185.967790206592014 > -186.860723909399354). You may want to try with a higher value of support_fraction (current value: 0.636).
/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) (-187.027667649929924 > -232.874879442697932). You may want to try with a higher value of support_fraction (current value: 0.636).
/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) (-187.245199678934000 > -188.235183828649895). You may want to try with a higher value of support_fraction (current value: 0.641).
/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) (-243.827558360744348 > -245.229687535958874). You may want to try with a higher value of support_fraction (current value: 0.636).
/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) (-150.047263806656105 > -150.375209702226073). You may want to try with a higher value of support_fraction (current value: 0.636).
/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) (-149.456881593174103 > -151.158921977546271). You may want to try with a higher value of support_fraction (current value: 0.643).
/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) (-149.295580365296701 > -149.735832300159160). You may want to try with a higher value of support_fraction (current value: 0.643).
/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) (-186.454390160242809 > -187.967407615396837). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-216.122414541530162 > -252.393054350799702). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-123.375389217556446 > -182.605034337143536). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-218.492045712165634 > -218.800997105276821). You may want to try with a higher value of support_fraction (current value: 0.638).
/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) (-151.598128779901003 > -240.624915980522957). You may want to try with a higher value of support_fraction (current value: 0.568).
/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) (-125.873034050624767 > -125.903833583602520). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-125.873034050624767 > -125.903833583602520). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-131.213785850860774 > -131.906933031420749). You may want to try with a higher value of support_fraction (current value: 0.605).
/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) (-132.427163604965585 > -133.525775893634062). You may want to try with a higher value of support_fraction (current value: 0.605).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-7.177237075045912 > -42.771653969298214). You may want to try with a higher value of support_fraction (current value: 0.519).
/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) (-43.482208723044977 > -77.331573854984939). You may want to try with a higher value of support_fraction (current value: 0.552).
/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) (-43.482208723044977 > -77.331573854984939). You may want to try with a higher value of support_fraction (current value: 0.552).
/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) (-113.961212225582187 > -145.292859607009802). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-94.152529155465075 > -119.525847258504911). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-93.901148569912692 > -121.281942022442962). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-100.399564995400581 > -115.761862660531889). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-97.804101368911404 > -113.615725786763903). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-100.399564995400581 > -116.167327768640078). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-100.399564995400581 > -115.761862660531833). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-112.656154020278152 > -129.043076991734665). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-112.780442960527736 > -161.947991253161803). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-112.656154020278152 > -129.043076991734665). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-112.780442960527736 > -161.947991253161803). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-98.762595013519217 > -160.513524629813503). You may want to try with a higher value of support_fraction (current value: 0.586).
/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) (-92.665377433164537 > -154.470160475547260). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-92.691982891652643 > -147.623760776100738). You may want to try with a higher value of support_fraction (current value: 0.575).
/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) (-79.843126744754599 > -135.038900348620672). You may want to try with a higher value of support_fraction (current value: 0.563).
/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) (-79.952744547364389 > -138.610508969809899). You may want to try with a higher value of support_fraction (current value: 0.563).
/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) (-79.702287442095582 > -136.566608280390511). You may want to try with a higher value of support_fraction (current value: 0.563).
/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) (-42.087058070157461 > -99.195038217804552). 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) (-99.576860204827057 > -100.415135094308752). 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) (-98.861567027594091 > -99.249487701140026). 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) (-99.438243377161655 > -99.576860204827057). 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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-6.803515704076716 > -42.617803626131263). You may want to try with a higher value of support_fraction (current value: 0.521).
/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) (-118.134338508007446 > -118.569640224890236). You may want to try with a higher value of support_fraction (current value: 0.590).
/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) (-63.427706748603164 > -89.504749282571467). You may want to try with a higher value of support_fraction (current value: 0.563).
2026-06-03 04:44:13,878 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-03 04:44:13,879 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get ploidy, all chromosomes
/opt/venv/lib/python3.12/site-packages/cnv_pipe/sca/pipeline.py:302: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/sca/pipeline.py:303: RuntimeWarning: Mean of empty slice
/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='A23FG3YLT4_1__sex_calls.png'>
/opt/venv/lib/python3.12/site-packages/plotnine/layer.py:374: PlotnineWarning: geom_point : Removed 9 rows containing missing values.
2026-06-03 04:45:13,217 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-03 04:45:13,217 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-03 04:45:16,244 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-03 04:45:16,244 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-03 04:45:16,244 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-03 04:45:16,254 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 164799
2026-06-03 04:45:16,474 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 25698
2026-06-03 04:45:16,705 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 1561
2026-06-03 04:45:16,941 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 299
2026-06-03 04:45:17,151 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 74
2026-06-03 04:45:17,365 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 20
2026-06-03 04:45:17,604 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 4
2026-06-03 04:45:17,841 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 2
2026-06-03 04:45:18,063 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 2
2026-06-03 04:45:18,277 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 1
2026-06-03 04:45:18,506 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 2
2026-06-03 04:45:18,735 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 0
2026-06-03 04:45:18,975 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 9657
2026-06-03 04:45:18,979 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 1528
2026-06-03 04:45:18,983 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 155
2026-06-03 04:45:18,987 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 26
2026-06-03 04:45:18,992 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 15
2026-06-03 04:45:18,995 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 6
2026-06-03 04:45:18,998 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 1
2026-06-03 04:45:19,002 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 1
2026-06-03 04:45:19,005 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 0
2026-06-03 04:45:19,009 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-03 04:45:19,009 - 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-23.125748056340754 > -49.967847233152426). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-23.125748056340754 > -49.967847233152426). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-51.501880405148768 > -51.943558915818045). 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) (-23.125748056340754 > -49.967847233152426). 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) (-12.762772471111640 > -46.765737529906360). You may want to try with a higher value of support_fraction (current value: 0.535).
/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) (-10.727952449013541 > -45.342550189113709). You may want to try with a higher value of support_fraction (current value: 0.535).
/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) (-12.762772471111640 > -46.765737529906360). You may want to try with a higher value of support_fraction (current value: 0.535).
/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) (-10.727952449013541 > -45.342550189113709). You may want to try with a higher value of support_fraction (current value: 0.535).
/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) (-33.364489739155921 > -100.373165142717383). You may want to try with a higher value of support_fraction (current value: 0.574).
2026-06-03 04:45:53,439 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-03 04:45:53,439 - 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:239: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:239: 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
/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
2026-06-03 04:45:54,887 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-03 04:45:54,887 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-03 04:46:27,315 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-03 04:46:27,316 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1213: RuntimeWarning: Mean of empty slice
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:316: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
/opt/venv/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1997: RuntimeWarning: Degrees of freedom <= 0 for slice.
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:318: SmallSampleWarning: One or more sample arguments is too small; all returned values will be NaN. See documentation for sample size requirements.
2026-06-03 04:46:31,424 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-03 04:46:31,425 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-03 04:46:31,435 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete