mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-530n_p77 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 04:21:47,948 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-03 04:22:05,570 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-03 04:22:05,575 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-03 04:22:05,675 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1396152
2026-06-03 04:22:10,653 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 538283
2026-06-03 04:22:15,550 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 201623
2026-06-03 04:22:20,557 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 118923
2026-06-03 04:22:25,579 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 76029
2026-06-03 04:22:30,535 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 51098
2026-06-03 04:22:35,473 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 34681
2026-06-03 04:22:40,484 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 24371
2026-06-03 04:22:45,494 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 17541
2026-06-03 04:22:50,528 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 12803
2026-06-03 04:22:55,487 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 9779
2026-06-03 04:23:00,546 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 7521
2026-06-03 04:23:05,561 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 5619
2026-06-03 04:23:10,638 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 13, outliers: 4602
2026-06-03 04:23:15,695 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 14, outliers: 3662
2026-06-03 04:23:20,733 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 15, outliers: 3049
2026-06-03 04:23:25,751 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 16, outliers: 2504
2026-06-03 04:23:30,773 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 17, outliers: 1951
2026-06-03 04:23:35,812 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 18, outliers: 1571
2026-06-03 04:23:40,808 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 19, outliers: 1407
2026-06-03 04:23:45,805 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 20, outliers: 1269
2026-06-03 04:23:50,842 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 21, outliers: 1110
2026-06-03 04:23:55,889 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 22, outliers: 849
2026-06-03 04:24:00,938 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 23, outliers: 673
2026-06-03 04:24:05,960 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 24, outliers: 612
2026-06-03 04:24:11,029 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-03 04:24:11,029 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-03 04:24:15,156 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-03 04:24:15,159 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-03 04:24:15,262 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1396152
2026-06-03 04:24:20,595 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 536412
2026-06-03 04:24:25,967 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 199224
2026-06-03 04:24:31,412 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 116238
2026-06-03 04:24:36,804 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 73030
2026-06-03 04:24:42,229 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 48436
2026-06-03 04:24:47,629 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 32251
2026-06-03 04:24:52,948 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 21981
2026-06-03 04:24:58,350 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 15239
2026-06-03 04:25:03,711 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 10737
2026-06-03 04:25:09,027 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 7658
2026-06-03 04:25:14,284 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 5588
2026-06-03 04:25:19,519 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 12, outliers: 3970
2026-06-03 04:25:24,861 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 13, outliers: 2835
2026-06-03 04:25:30,229 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 14, outliers: 2149
2026-06-03 04:25:35,762 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 15, outliers: 1669
2026-06-03 04:25:41,143 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 16, outliers: 1145
2026-06-03 04:25:46,616 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 17, outliers: 915
2026-06-03 04:25:52,150 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 18, outliers: 684
2026-06-03 04:25:57,525 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 19, outliers: 462
2026-06-03 04:26:02,847 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 20, outliers: 363
2026-06-03 04:26:08,606 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 21, outliers: 325
2026-06-03 04:26:13,963 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 22, outliers: 189
2026-06-03 04:26:19,345 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 23, outliers: 160
2026-06-03 04:26:24,704 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 24, outliers: 90
2026-06-03 04:26:30,043 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-03 04:26:30,044 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-03 04:27:13,361 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-03 04:27:13,361 - 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) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-10.875424308090729 > -48.359327692326460). You may want to try with a higher value of support_fraction (current value: 0.534).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.534593962721033 > -129.155098868796102). You may want to try with a higher value of support_fraction (current value: 0.557).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.534593962721033 > -129.155098868796102). You may want to try with a higher value of support_fraction (current value: 0.557).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-48.195054025128023 > -80.102018883104407). You may want to try with a higher value of support_fraction (current value: 0.569).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-40.901220843262067 > -105.511790385736361). 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) (-40.901220843262067 > -105.511790385736361). 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) (-120.325160409841914 > -151.921057067728668). You may want to try with a higher value of support_fraction (current value: 0.609).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-70.435998429548604 > -133.940209610394731). You may want to try with a higher value of support_fraction (current value: 0.607).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-68.555449073301133 > -69.681262538581819). 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) (-66.714069833589605 > -66.933763885451086). 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) (-68.555449073301133 > -69.681262538581819). 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) (-68.555449073301133 > -69.681262538581819). 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) (-66.714069833589605 > -66.933763885451086). 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) (-68.555449073301133 > -69.681262538581819). 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) (-68.555449073301133 > -69.681262538581819). 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) (-66.714069833589605 > -66.933763885451086). 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) (-68.555449073301133 > -69.681262538581819). 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) (-9.232688481134247 > -44.045670067546425). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.232688481134247 > -44.045670067546425). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.232688481134247 > -44.045670067546425). You may want to try with a higher value of support_fraction (current value: 0.529).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-169.141573338326509 > -172.043669064954940). 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) (-170.191075791598593 > -170.421096640561700). 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) (-169.434243797000363 > -171.891259658959825). 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) (-191.648404194029467 > -192.550399629093391). You may want to try with a higher value of support_fraction (current value: 0.606).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.890821241532734 > -193.996864949078542). You may want to try with a higher value of support_fraction (current value: 0.606).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-191.671133035226148 > -191.947150921579066). You may want to try with a higher value of support_fraction (current value: 0.597).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-194.129858633205004 > -194.145546141588454). You may want to try with a higher value of support_fraction (current value: 0.597).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.167443155328115 > -46.845436757181197). You may want to try with a higher value of support_fraction (current value: 0.545).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-54.896641257452515 > -120.115091648486512). 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) (-41.046711705443457 > -95.602491795759036). 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) (-143.922553060133168 > -148.580227067295340). You may want to try with a higher value of support_fraction (current value: 0.621).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-85.296848390061683 > -147.561008504120849). 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) (-84.899374791750873 > -149.643196377480194). 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) (-146.568851018315939 > -152.807175646398946). You may want to try with a higher value of support_fraction (current value: 0.621).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-181.773850825017973 > -185.782109559204628). You may want to try with a higher value of support_fraction (current value: 0.627).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-178.517773967883386 > -184.847889161790619). You may want to try with a higher value of support_fraction (current value: 0.621).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-182.657271802226376 > -195.758176033495005). 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) (-189.537652026011841 > -197.722175062518602). 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) (-182.657271802226376 > -195.758176033495005). 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) (-189.537652026011841 > -197.722175062518602). 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) (-50.118449187263188 > -81.430068373339537). 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) (-50.118449187263188 > -81.430068373339537). 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) (-50.118449187263188 > -81.430068373339537). 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) (-50.118449187263188 > -81.430068373339537). 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) (-50.118449187263188 > -81.430068373339537). 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) (-50.118449187263188 > -81.430068373339537). 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) (-158.433956718178194 > -158.814291198174203). You may want to try with a higher value of support_fraction (current value: 0.627).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-161.114286888796101 > -161.415448492853471). You may want to try with a higher value of support_fraction (current value: 0.627).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.772041629148589 > -159.968897559821130). You may want to try with a higher value of support_fraction (current value: 0.627).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-192.232196236556234 > -192.860804896491572). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-162.901684994327070 > -163.582135406944928). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-211.216155927716130 > -213.854707662429064). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-159.131275517986097 > -159.843324377324336). You may want to try with a higher value of support_fraction (current value: 0.612).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-154.510337199926994 > -154.524611717634514). You may want to try with a higher value of support_fraction (current value: 0.606).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-154.510337199926994 > -154.524611717634514). You may want to try with a higher value of support_fraction (current value: 0.606).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-50.368286783926465 > -53.504720153079816). 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) (-50.368286783926465 > -53.504720153079816). 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) (-50.368286783926465 > -53.504720153079816). 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) (-21.413479401690477 > -50.368286783926465). 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) (-21.413479401690477 > -50.368286783926465). 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) (-21.413479401690477 > -50.368286783926465). 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) (-21.413479401690477 > -50.368286783926465). 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) (-53.504720153079816 > -53.860106873071445). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). 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) (-9.702395881779420 > -46.703479440082276). You may want to try with a higher value of support_fraction (current value: 0.542).
2026-06-03 04:30:56,133 - cnv_pipe.cnv_pipe.batch.ess - WARNING - No valid samples remain for probe 433606 after NaN filtering. Assigning default weight of 1.0.
/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: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: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: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: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: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: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: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: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:793: UserWarning: The covariance matrix associated to your dataset is not full rank
2026-06-03 04:31:02,538 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (3) compared to nearby probes (3) for probe 20465. MinCovDet requires more samples than features.
2026-06-03 04:31:02,539 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (3) compared to nearby probes (3) for probe 20466. MinCovDet requires more samples than features.
2026-06-03 04:31:02,539 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (3) compared to nearby probes (3) for probe 20467. 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) (-43.348490115668994 > -66.509620148796003). You may want to try with a higher value of support_fraction (current value: 0.569).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-87.891492790984245 > -89.533744265151824). You may want to try with a higher value of support_fraction (current value: 0.574).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-98.770375651570731 > -99.221609178129299). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-97.726849030462830 > -98.364426359882629). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-96.450350092272032 > -96.984432578187523). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-97.270317124323469 > -98.629943238467064). You may want to try with a higher value of support_fraction (current value: 0.604).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-196.534288835263936 > -197.837329907082619). 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) (-193.065668523776367 > -197.665387886458490). 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) (-164.578148728585063 > -166.663374130157479). 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) (-194.617570031188905 > -198.996649834024765). 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) (-194.834728444396745 > -196.520395473292552). 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) (-170.257789299632691 > -170.348784001652234). 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) (-196.237690844529908 > -198.455541990878316). 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) (-196.534288835263936 > -197.837329907082619). 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) (-193.065668523776367 > -197.665387886458490). 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) (-164.578148728585063 > -166.663374130157479). 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) (-194.617570031188905 > -198.996649834024765). 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) (-194.834728444396745 > -196.520395473292552). 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) (-170.257789299632691 > -170.348784001652234). 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) (-196.237690844529908 > -198.455541990878316). 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) (-196.534288835263936 > -197.837329907082619). 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) (-193.065668523776367 > -197.665387886458490). 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) (-164.578148728585063 > -166.663374130157479). 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) (-194.617570031188905 > -198.996649834024765). 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) (-194.834728444396745 > -196.520395473292552). 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) (-170.257789299632691 > -170.348784001652234). 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) (-196.237690844529908 > -198.455541990878316). 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) (-199.111952049346002 > -200.920494929548596). 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) (-203.698068027825883 > -203.975295460202261). 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) (-242.800843740769977 > -244.548246074351766). 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) (-241.150043466673509 > -241.635895041913443). 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) (-242.670934790718377 > -243.925458776129773). 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) (-38.963332246128793 > -107.970473387704146). 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) (-38.963332246128793 > -107.970473387704146). 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) (-137.212411692997733 > -137.284708325366807). You may want to try with a higher value of support_fraction (current value: 0.597).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-137.581425999195886 > -241.075206949735076). You may want to try with a higher value of support_fraction (current value: 0.611).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-141.760185339452903 > -142.337412890056299). You may want to try with a higher value of support_fraction (current value: 0.611).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py: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: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) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.443400101600105 > -110.705264243440126). You may want to try with a higher value of support_fraction (current value: 0.628).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-26.619598019739691 > -53.849516225456981). You may want to try with a higher value of support_fraction (current value: 0.536).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-26.619598019739691 > -53.849516225456981). You may want to try with a higher value of support_fraction (current value: 0.536).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-102.073871049559571 > -103.273582614090060). You may want to try with a higher value of support_fraction (current value: 0.565).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.038203688838868 > -43.707659680749373). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.038203688838868 > -43.707659680749373). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.038203688838868 > -43.707659680749373). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.038203688838868 > -43.707659680749373). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.038203688838868 > -43.707659680749373). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.477845968642566 > -43.677297214152560). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.477845968642566 > -43.677297214152560). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.477845968642566 > -43.677297214152560). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.477845968642566 > -43.677297214152560). You may want to try with a higher value of support_fraction (current value: 0.525).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.494295697569001 > -45.524047548878478). 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) (-8.494295697569001 > -45.524047548878478). You may want to try with a higher value of support_fraction (current value: 0.535).
2026-06-03 04:38:01,246 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-03 04:38:01,247 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get ploidy, all chromosomes
/opt/venv/lib/python3.12/site-packages/plotnine/ggplot.py:623: PlotnineWarning: Saving 6 x 5 in image.
/opt/venv/lib/python3.12/site-packages/plotnine/ggplot.py:624: PlotnineWarning: Filename: <_io.BufferedWriter name='A23H3NYLT3_1__sex_calls.png'>
2026-06-03 04:38:36,172 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-03 04:38:36,172 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-03 04:38:37,228 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-03 04:38:37,229 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-03 04:38:37,229 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-03 04:38:37,233 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-03 04:38:37,325 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 26640
2026-06-03 04:38:37,409 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 1208
2026-06-03 04:38:37,488 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 228
2026-06-03 04:38:37,566 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 102
2026-06-03 04:38:37,644 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 32
2026-06-03 04:38:37,722 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 10
2026-06-03 04:38:37,800 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 7
2026-06-03 04:38:37,878 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 2
2026-06-03 04:38:37,957 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 0
2026-06-03 04:38:38,038 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-03 04:38:38,041 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 1027
2026-06-03 04:38:38,043 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 104
2026-06-03 04:38:38,045 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 28
2026-06-03 04:38:38,048 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 14
2026-06-03 04:38:38,050 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 5
2026-06-03 04:38:38,052 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 1
2026-06-03 04:38:38,055 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 0
2026-06-03 04:38:38,058 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-03 04:38:38,058 - 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: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) (-53.099437055813794 > -53.751603893076542). 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) (-53.099437055813794 > -53.281600264720112). 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) (-53.099437055813794 > -53.751603893076542). 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) (-53.099437055813794 > -53.281600264720112). 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) (-53.099437055813794 > -53.751603893076542). 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) (-53.099437055813794 > -53.281600264720112). 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: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: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
2026-06-03 04:38:49,004 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9841. MinCovDet requires more samples than features.
2026-06-03 04:38:49,005 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9842. MinCovDet requires more samples than features.
2026-06-03 04:38:49,036 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9844. MinCovDet requires more samples than features.
2026-06-03 04:38:49,037 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9845. MinCovDet requires more samples than features.
2026-06-03 04:38:49,038 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9846. MinCovDet requires more samples than features.
2026-06-03 04:38:49,038 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9847. MinCovDet requires more samples than features.
2026-06-03 04:38:49,039 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9848. MinCovDet requires more samples than features.
2026-06-03 04:38:49,040 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9849. MinCovDet requires more samples than features.
2026-06-03 04:38:49,040 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (39) for probe 9850. MinCovDet requires more samples than features.
2026-06-03 04:38:49,041 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9851. MinCovDet requires more samples than features.
2026-06-03 04:38:49,042 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9852. MinCovDet requires more samples than features.
2026-06-03 04:38:49,042 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (38) compared to nearby probes (38) for probe 9853. MinCovDet requires more samples than features.
2026-06-03 04:38:49,043 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (36) compared to nearby probes (37) for probe 9854. MinCovDet requires more samples than features.
2026-06-03 04:38:49,044 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (38) for probe 9855. MinCovDet requires more samples than features.
2026-06-03 04:38:49,044 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (37) for probe 9856. MinCovDet requires more samples than features.
2026-06-03 04:38:49,045 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (38) for probe 9857. MinCovDet requires more samples than features.
2026-06-03 04:38:49,046 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (37) for probe 9858. MinCovDet requires more samples than features.
2026-06-03 04:38:49,046 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (39) for probe 9859. MinCovDet requires more samples than features.
2026-06-03 04:38:49,047 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (39) for probe 9860. MinCovDet requires more samples than features.
2026-06-03 04:38:49,047 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (37) for probe 9861. MinCovDet requires more samples than features.
2026-06-03 04:38:49,048 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (35) compared to nearby probes (36) for probe 9862. 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) (-80.995735385821590 > -85.848706058710462). You may want to try with a higher value of support_fraction (current value: 0.615).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-80.995735385821590 > -85.848706089364242). You may want to try with a higher value of support_fraction (current value: 0.615).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-80.995735385821590 > -85.848706058710462). You may want to try with a higher value of support_fraction (current value: 0.615).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-80.995735385821590 > -85.848706089364242). You may want to try with a higher value of support_fraction (current value: 0.615).
2026-06-03 04:39:05,091 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-03 04:39:05,091 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get the final double norm values, adjusting for ploidies
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: divide by zero encountered in divide
/opt/venv/lib/python3.12/site-packages/cnv_pipe/batch/preprocess.py:249: RuntimeWarning: invalid value encountered in divide
2026-06-03 04:39:05,973 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-03 04:39:05,973 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-03 04:39:22,762 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-03 04:39:22,762 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-03 04:39:24,862 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-03 04:39:24,862 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-03 04:39:24,868 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete