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==> STAGING COMPLETE (77 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-axgsj7ya 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 04:23:17,236 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Load count data for processing
2026-06-03 04:23:34,397 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Data loaded
2026-06-03 04:23:34,403 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Find low probe mask, low sample mask, and 2D outlier mask. Autosomes only.
2026-06-03 04:23:34,493 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1396152
2026-06-03 04:23:39,376 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 166112
2026-06-03 04:23:44,268 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 9683
2026-06-03 04:23:49,122 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 1818
2026-06-03 04:23:53,863 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 681
2026-06-03 04:23:58,606 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 235
2026-06-03 04:24:03,363 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 97
2026-06-03 04:24:08,177 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 40
2026-06-03 04:24:12,963 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 25
2026-06-03 04:24:17,760 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 8
2026-06-03 04:24:22,561 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 1
2026-06-03 04:24:27,374 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 11, outliers: 0
2026-06-03 04:24:32,152 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained
2026-06-03 04:24:32,152 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Correct counts based on melting temperature
2026-06-03 04:24:36,154 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained
2026-06-03 04:24:36,157 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Refind masks with melting-temperature corrected counts. Autosomes only.
2026-06-03 04:24:36,251 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 1396152
2026-06-03 04:24:41,352 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 165164
2026-06-03 04:24:46,456 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 9626
2026-06-03 04:24:51,613 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 1860
2026-06-03 04:24:56,810 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 765
2026-06-03 04:25:02,244 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 211
2026-06-03 04:25:07,689 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 98
2026-06-03 04:25:12,887 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 33
2026-06-03 04:25:18,284 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 8, outliers: 14
2026-06-03 04:25:23,688 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 9, outliers: 4
2026-06-03 04:25:29,209 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 10, outliers: 0
2026-06-03 04:25:34,855 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks obtained, from melting-temperature corrected counts
2026-06-03 04:25:34,856 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Redo melting-temperature correction with new masks
2026-06-03 04:26:20,121 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Corrected counts obtained, using second round of masks
2026-06-03 04:26:20,121 - 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) (-120.375262933290387 > -122.896389194692517). 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) (-105.769967423309396 > -106.258685353720239). 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) (-102.426000901191060 > -171.304540308985622). 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) (-208.063597512117923 > -208.954305294467105). 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) (-206.312460849859434 > -211.080430204291531). 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) (-209.729051049996485 > -210.767520677896215). 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) (-208.063597512117923 > -208.954305294467105). 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) (-206.312460849859434 > -211.080430204291531). 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) (-209.729051049996485 > -210.767520677896215). 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) (-290.292871361745256 > -295.956616060577176). 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) (-295.086871105312071 > -297.883850724420768). 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) (-288.571743237085855 > -292.875846055604654). 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) (-290.292871361745256 > -297.151207511631412). 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) (-292.643766576760243 > -293.210984678069565). 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) (-254.869255209778032 > -257.772252230201730). 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) (-258.147464679227824 > -258.319409484724986). 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) (-258.147464679227824 > -259.465622021258923). 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) (-256.428460368763979 > -263.506838150537988). 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) (-224.814687505655741 > -225.819580415886691). 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) (-223.569773837519421 > -228.003221287558432). 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) (-228.046788550509916 > -229.636070368357508). 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) (-109.244280817454182 > -109.651659238143750). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-163.866432306310429 > -164.775374414390399). 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) (-164.594936657106217 > -166.043161058055887). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-101.871608443733066 > -167.555518719888227). 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) (-102.436039375069114 > -167.056691312267958). 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) (-147.614111241883705 > -173.841294060987991). You may want to try with a higher value of support_fraction (current value: 0.594).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-178.653062576102315 > -179.403400397100199). 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) (-99.639201217597204 > -100.032307955769141). 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) (-94.658796922680310 > -95.169311110482781). 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) (-72.672905305587776 > -106.275473595472036). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-72.672905305587776 > -106.275473595472036). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-43.862686996901218 > -76.791536768115520). 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) (-43.862686996901218 > -76.791536768115520). 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) (-43.862686996901218 > -76.791536768115520). 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) (-43.862686996901218 > -76.791536768115520). 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) (-142.800675466466600 > -143.747481742264881). You may want to try with a higher value of support_fraction (current value: 0.620).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-146.539221655223884 > -207.435882313155332). You may want to try with a higher value of support_fraction (current value: 0.632).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-144.979484706954423 > -202.342357731689930). You may want to try with a higher value of support_fraction (current value: 0.629).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-227.347965603137141 > -231.876811356827915). You may want to try with a higher value of support_fraction (current value: 0.625).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-183.253523170105012 > -217.269570596618280). You may want to try with a higher value of support_fraction (current value: 0.625).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-183.253523170105012 > -217.269570596618280). You may want to try with a higher value of support_fraction (current value: 0.625).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-105.657217869816080 > -167.221290569101797). 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) (-107.255599905058887 > -169.862955317771650). 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) (-107.580746931284338 > -167.970667162675909). 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) (-106.088404291469800 > -167.939538348849908). 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) (-107.015393493379506 > -169.809256273088295). 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) (-105.879854683078889 > -165.857045903810956). 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) (-105.657217869816080 > -167.221290569101797). 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) (-107.255599905058887 > -169.862955317771650). 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) (-107.580746931284338 > -167.970667162675909). 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) (-106.088404291469800 > -167.939538348849908). 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) (-107.015393493379506 > -169.809256273088295). 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) (-105.879854683078889 > -165.857045903810956). 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) (-122.890363035343739 > -158.335167961561922). 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) (-122.890363035343739 > -158.335167961561922). 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) (-122.890363035343739 > -158.335167961561922). You may want to try with a higher value of support_fraction (current value: 0.569).
2026-06-03 04:29:45,332 - cnv_pipe.cnv_pipe.batch.ess - WARNING - No valid samples remain for probe 433606 after NaN filtering. Assigning default weight of 1.0.
2026-06-03 04:29:45,332 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (5) compared to nearby probes (10) for probe 433607. MinCovDet requires more samples than features.
/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:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-261.398181807596245 > -354.050114166509559). You may want to try with a higher value of support_fraction (current value: 0.667).
/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:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-79.462135181531067 > -97.118959509444750). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-61.369348072701854 > -198.575863470558147). 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) (-127.572808068579462 > -128.832113633582424). 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) (-171.686822044098108 > -173.390639725834319). 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) (-140.775174959149183 > -141.158434981111697). 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) (-129.549484782188870 > -156.668591414352306). 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) (-129.549484782188870 > -156.668591414352306). 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) (-129.214652507594280 > -129.743147609241817). 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) (-129.214652507594280 > -129.743147609241817). 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) (-161.912385071292107 > -162.177675306315251). 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) (-161.912385071292107 > -162.177675306315251). 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) (-134.513111839256482 > -135.317719481697736). 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: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) (-40.477520508051519 > -65.153159903373904). 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: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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-75.807216087955354 > -142.958482194911824). 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) (-69.141517810592475 > -102.326111362709355). 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) (-6.197430729187499 > -42.317430818734074). 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) (-6.197430729187499 > -42.317430818734074). 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) (-34.974331568366530 > -117.187195066123692). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-34.974331568366530 > -117.187195066123692). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-34.974331568366530 > -117.187195066123692). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.124798183961122 > -44.193693991292768). You may want to try with a higher value of support_fraction (current value: 0.531).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-8.213992822265208 > -43.863468156487365). 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) (-8.213992822265208 > -43.863468156487365). 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) (-8.213992822265208 > -43.863468156487365). 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) (-8.213992822265208 > -43.863468156487365). 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) (-8.213992822265208 > -43.863468156487365). 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) (-8.213992822265208 > -43.863468156487365). 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) (-121.826142995567523 > -123.206193669840815). 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) (-114.342934111764649 > -114.460478791638309). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-118.350055977927525 > -119.573831401915612). 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) (-114.650994392063168 > -115.903757360592550). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.830724893772157 > -55.811400414586927). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.830724893772157 > -55.811400414587993). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.830724893772157 > -55.811400414586927). 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) (-28.802933990740392 > -55.105926057795664). 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) (-28.830724893772157 > -55.811400414587993). 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) (-100.215110276275041 > -102.884249318866907). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-98.405140882904774 > -99.996871344825337). You may want to try with a higher value of support_fraction (current value: 0.583).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-93.054193439990499 > -122.166315008246798). 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) (-93.168314797300113 > -121.784913867173969). 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) (-93.054193439990499 > -122.166315008246798). 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) (-93.168314797300113 > -121.784913867173969). You may want to try with a higher value of support_fraction (current value: 0.569).
2026-06-03 04:35:46,779 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size obtained
2026-06-03 04:35:46,779 - 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='A237YLNLT3_1__sex_calls.png'>
2026-06-03 04:36:22,430 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Ploidy obtained
2026-06-03 04:36:22,430 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get sample medians adjusting for ploidy and effective sample size
2026-06-03 04:36:23,471 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample medians obtained
2026-06-03 04:36:23,471 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Use ploidy information to get the proper masks for chrX and chrY
2026-06-03 04:36:23,471 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - 
2026-06-03 04:36:23,476 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-03 04:36:23,569 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 7673
2026-06-03 04:36:23,651 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 666
2026-06-03 04:36:23,730 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 182
2026-06-03 04:36:23,811 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 63
2026-06-03 04:36:23,890 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 41
2026-06-03 04:36:23,972 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 3
2026-06-03 04:36:24,051 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 0
2026-06-03 04:36:24,136 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 0, outliers: 0
2026-06-03 04:36:24,138 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 1, outliers: 931
2026-06-03 04:36:24,141 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 2, outliers: 88
2026-06-03 04:36:24,143 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 3, outliers: 14
2026-06-03 04:36:24,145 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 4, outliers: 4
2026-06-03 04:36:24,148 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 5, outliers: 2
2026-06-03 04:36:24,150 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 6, outliers: 1
2026-06-03 04:36:24,152 - cnv_pipe.cnv_pipe.batch.mask - INFO - Iteration 7, outliers: 0
2026-06-03 04:36:24,156 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Masks for chrX and chrY obtained
2026-06-03 04:36:24,156 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Get effective sample size for chrX and chrY
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-11.010329872489368 > -46.692905276525217). 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) (-9.212153338367003 > -45.660961639302130). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.212153338367003 > -45.660961639302130). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.212153338367003 > -45.660961639302130). You may want to try with a higher value of support_fraction (current value: 0.560).
/opt/venv/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.212153338367003 > -45.660961639302130). You may want to try with a higher value of support_fraction (current value: 0.560).
/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:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-98.404993352963501 > -128.031536096198579). 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) (-98.404993352963501 > -128.031536096198579). 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) (-98.404993352963501 > -128.031536096198579). 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) (-98.404993352963501 > -128.031536096198579). 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) (-37.079827973086864 > -127.066835354785269). 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) (-34.099604384180346 > -126.859027498777039). You may want to try with a higher value of support_fraction (current value: 0.575).
2026-06-03 04:36:46,476 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Effective sample size for chrX and chrY obtained
2026-06-03 04:36:46,476 - 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 04:36:47,344 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Double norm values obtained
2026-06-03 04:36:47,344 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Format and write the data for sample-probe combinations
2026-06-03 04:37:04,289 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-probe data written
2026-06-03 04:37:04,289 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics. Calculating, formatting, and saving
2026-06-03 04:37:06,469 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Sample-level metrics written
2026-06-03 04:37:06,470 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Save ploidy estimates
2026-06-03 04:37:06,476 - cnv_pipe.cnv_pipe.batch.preprocess - INFO - Batch pre-processing complete