2025-06-12 13:36:00,582::INFO::main: Starting joint PCA 2025-06-12 13:36:10,710::INFO::__init__: JointPCADecomposer :: configuration: ==================== Joint PCA Configuration ==================== mcools : - day00_ESC_pool.hg38.mapq_30.100.mcool - day02_mesoderm_pool.hg38.mapq_30.100.mcool - day05_cardiacMesoderm_pool.hg38.mapq_30.100.mcool - day07_cardiacProgenitor_pool.hg38.mapq_30.100.mcool - day15_primativeCardiomyocyte_pool.hg38.mapq_30.100.mcool - day80_ventricularCardiomyocyte_pool.hg38.mapq_30.100.mcool - DE-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool - DE_pool.hg38.mapq_30.100.mcool - ENCFF004YZQ.mcool - ENCFF009ONH.mcool - ENCFF019YVI.mcool - ENCFF029UAL.mcool - ENCFF035BLF.mcool - ENCFF044TCQ.mcool - ENCFF059WMS.mcool - ENCFF076LWH.mcool - ENCFF081PMO.mcool - ENCFF094KKX.mcool - ENCFF136XCV.mcool - ENCFF140ROU.mcool - ENCFF149IHN.mcool - ENCFF176LIZ.mcool - ENCFF185AYZ.mcool - ENCFF193CQL.mcool - ENCFF197OWW.mcool - ENCFF224HKR.mcool - ENCFF235LCO.mcool - ENCFF251VFA.mcool - ENCFF252ANV.mcool - ENCFF273XBU.mcool - ENCFF284OEA.mcool - ENCFF309UNV.mcool - ENCFF333WCK.mcool - ENCFF355NFJ.mcool - ENCFF355VJW.mcool - ENCFF395INO.mcool - ENCFF417GBZ.mcool - ENCFF442IGJ.mcool - ENCFF458VBB.mcool - ENCFF493SFI.mcool - ENCFF493YNC.mcool - ENCFF496GEU.mcool - ENCFF499BVX.mcool - ENCFF515ZBF.mcool - ENCFF520GFL.mcool - ENCFF545GBW.mcool - ENCFF556RLR.mcool - ENCFF558DYU.mcool - ENCFF571GTF.mcool - ENCFF579CAR.mcool - ENCFF586MQY.mcool - ENCFF591MHA.mcool - ENCFF605CEN.mcool - ENCFF614IPZ.mcool - ENCFF625VNK.mcool - ENCFF628LQQ.mcool - ENCFF653HCO.mcool - ENCFF654YIQ.mcool - ENCFF660JWA.mcool - ENCFF663FRL.mcool - ENCFF684YCT.mcool - ENCFF687ATD.mcool - ENCFF700CYI.mcool - ENCFF705YZH.mcool - ENCFF711XSR.mcool - ENCFF736ITL.mcool - ENCFF782WVZ.mcool - ENCFF783KQI.mcool - ENCFF839VMS.mcool - ENCFF842DUO.mcool - ENCFF883XXW.mcool - ENCFF897KRI.mcool - ENCFF911AHQ.mcool - ENCFF925QIF.mcool - ENCFF943JRY.mcool - ENCFF952JZV.mcool - ENCFF958DWQ.mcool - ENCFF962EDB.mcool - ENCFF965BPU.mcool - ENCFF980NXK.mcool - ESC-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool - HB-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool - hESC_pool.hg38.mapq_30.100.mcool - iHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool - mHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool - PGT_pool.hg38.mapq_30.100.mcool - PH_pool.hg38.mapq_30.100.mcool - PP_pool.hg38.mapq_30.100.mcool - SC_Beta_pool.hg38.mapq_30.100.mcool resolution : 50000 assembly : hg38 output : output_2025_06_12_13_36 components : 32 chrom_limit : 22 method : PCA exclusion_list : blacklist.mad_max9.50000.bed percentile_top : 100.0 percentile_bottom : 0.0 batch_size : 20000 log_level : INFO =================================================================== 2025-06-12 13:36:10,728::INFO::get_chromosome_sizes: Loaded chromosome sizes for specified assembly: hg38 2025-06-12 13:36:10,728::INFO::get_chromosome_sizes: Chromosome sizes: name chr1 248956422 chr2 242193529 chr3 198295559 chr4 190214555 chr5 181538259 chr6 170805979 chr7 159345973 chr8 145138636 chr9 138394717 chr10 133797422 chr11 135086622 chr12 133275309 chr13 114364328 chr14 107043718 chr15 101991189 chr16 90338345 chr17 83257441 chr18 80373285 chr19 58617616 chr20 64444167 chr21 46709983 chr22 50818468 Name: length, dtype: int64 2025-06-12 13:36:10,729::INFO::set_union_bad_bins: Beginning to compute union set of NaN bins.. 2025-06-12 13:36:25,276::INFO::set_union_bad_bins: Loading exclusion list from: blacklist.mad_max9.50000.bed 2025-06-13 02:27:39,618::INFO::set_union_bad_bins: Loaded union set of bad bins in: 12:51:28.888889. 2025-06-13 02:27:39,621::INFO::set_union_bad_bins: Percent of bins that are bad: 12.213740458015268. 2025-06-13 02:27:40,450::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day00_ESC_pool.hg38.mapq_30.100.mcool'... 2025-06-13 02:27:40,490::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 03:08:21,056::INFO::decompose_cooler_file: Finished decomposition for 'day00_ESC_pool.hg38.mapq_30.100.mcool' in 0:40:40.605675. 2025-06-13 03:08:21,130::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day02_mesoderm_pool.hg38.mapq_30.100.mcool'... 2025-06-13 03:08:21,244::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 03:50:28,894::INFO::decompose_cooler_file: Finished decomposition for 'day02_mesoderm_pool.hg38.mapq_30.100.mcool' in 0:42:07.764485. 2025-06-13 03:50:28,976::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day05_cardiacMesoderm_pool.hg38.mapq_30.100.mcool'... 2025-06-13 03:50:29,035::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 04:31:06,235::INFO::decompose_cooler_file: Finished decomposition for 'day05_cardiacMesoderm_pool.hg38.mapq_30.100.mcool' in 0:40:37.258921. 2025-06-13 04:31:06,308::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day07_cardiacProgenitor_pool.hg38.mapq_30.100.mcool'... 2025-06-13 04:31:06,356::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 05:14:09,106::INFO::decompose_cooler_file: Finished decomposition for 'day07_cardiacProgenitor_pool.hg38.mapq_30.100.mcool' in 0:43:02.797300. 2025-06-13 05:14:09,188::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day15_primativeCardiomyocyte_pool.hg38.mapq_30.100.mcool'... 2025-06-13 05:14:09,244::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 05:54:24,908::INFO::decompose_cooler_file: Finished decomposition for 'day15_primativeCardiomyocyte_pool.hg38.mapq_30.100.mcool' in 0:40:15.720257. 2025-06-13 05:54:24,982::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'day80_ventricularCardiomyocyte_pool.hg38.mapq_30.100.mcool'... 2025-06-13 05:54:25,032::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 06:35:41,610::INFO::decompose_cooler_file: Finished decomposition for 'day80_ventricularCardiomyocyte_pool.hg38.mapq_30.100.mcool' in 0:41:16.628237. 2025-06-13 06:35:41,684::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'DE-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-13 06:35:41,728::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 07:15:19,882::INFO::decompose_cooler_file: Finished decomposition for 'DE-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool' in 0:39:38.198457. 2025-06-13 07:15:19,965::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'DE_pool.hg38.mapq_30.100.mcool'... 2025-06-13 07:15:20,000::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 07:56:04,373::INFO::decompose_cooler_file: Finished decomposition for 'DE_pool.hg38.mapq_30.100.mcool' in 0:40:44.407618. 2025-06-13 07:56:04,454::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF004YZQ.mcool'... 2025-06-13 07:56:04,521::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 08:37:06,585::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF004YZQ.mcool' in 0:41:02.130771. 2025-06-13 08:37:06,668::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF009ONH.mcool'... 2025-06-13 08:37:06,723::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 09:19:48,567::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF009ONH.mcool' in 0:42:41.899210. 2025-06-13 09:19:48,642::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF019YVI.mcool'... 2025-06-13 09:19:48,697::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 09:59:39,161::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF019YVI.mcool' in 0:39:50.518850. 2025-06-13 09:59:39,243::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF029UAL.mcool'... 2025-06-13 09:59:39,302::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 10:41:40,660::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF029UAL.mcool' in 0:42:01.417236. 2025-06-13 10:41:40,742::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF035BLF.mcool'... 2025-06-13 10:41:40,805::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 11:20:52,540::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF035BLF.mcool' in 0:39:11.797353. 2025-06-13 11:20:52,621::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF044TCQ.mcool'... 2025-06-13 11:20:52,659::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 12:01:34,020::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF044TCQ.mcool' in 0:40:41.398712. 2025-06-13 12:01:34,094::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF059WMS.mcool'... 2025-06-13 12:01:34,130::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 12:42:58,915::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF059WMS.mcool' in 0:41:24.821019. 2025-06-13 12:42:58,989::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF076LWH.mcool'... 2025-06-13 12:42:59,040::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 13:23:02,049::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF076LWH.mcool' in 0:40:03.059945. 2025-06-13 13:23:02,131::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF081PMO.mcool'... 2025-06-13 13:23:02,187::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 14:05:08,954::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF081PMO.mcool' in 0:42:06.823775. 2025-06-13 14:05:09,036::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF094KKX.mcool'... 2025-06-13 14:05:09,087::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 14:45:41,789::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF094KKX.mcool' in 0:40:32.753097. 2025-06-13 14:45:41,864::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF136XCV.mcool'... 2025-06-13 14:45:41,913::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 15:24:27,652::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF136XCV.mcool' in 0:38:45.788792. 2025-06-13 15:24:27,727::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF140ROU.mcool'... 2025-06-13 15:24:27,776::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 16:06:38,095::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF140ROU.mcool' in 0:42:10.368404. 2025-06-13 16:06:38,169::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF149IHN.mcool'... 2025-06-13 16:06:38,208::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 16:46:13,072::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF149IHN.mcool' in 0:39:34.902004. 2025-06-13 16:46:13,156::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF176LIZ.mcool'... 2025-06-13 16:46:13,203::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 17:29:07,593::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF176LIZ.mcool' in 0:42:54.437752. 2025-06-13 17:29:07,676::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF185AYZ.mcool'... 2025-06-13 17:29:07,772::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 18:08:56,135::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF185AYZ.mcool' in 0:39:48.459194. 2025-06-13 18:08:56,209::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF193CQL.mcool'... 2025-06-13 18:08:56,274::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 18:47:56,851::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF193CQL.mcool' in 0:39:00.641449. 2025-06-13 18:47:56,925::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF197OWW.mcool'... 2025-06-13 18:47:56,977::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 19:29:20,291::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF197OWW.mcool' in 0:41:23.365785. 2025-06-13 19:29:20,365::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF224HKR.mcool'... 2025-06-13 19:29:20,419::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 20:10:21,168::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF224HKR.mcool' in 0:41:00.803393. 2025-06-13 20:10:21,244::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF235LCO.mcool'... 2025-06-13 20:10:21,304::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 20:52:48,966::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF235LCO.mcool' in 0:42:27.722400. 2025-06-13 20:52:49,048::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF251VFA.mcool'... 2025-06-13 20:52:49,110::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 21:34:22,608::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF251VFA.mcool' in 0:41:33.559651. 2025-06-13 21:34:22,682::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF252ANV.mcool'... 2025-06-13 21:34:22,739::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 22:16:33,232::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF252ANV.mcool' in 0:42:10.549831. 2025-06-13 22:16:33,314::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF273XBU.mcool'... 2025-06-13 22:16:33,364::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 22:57:27,983::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF273XBU.mcool' in 0:40:54.668665. 2025-06-13 22:57:28,056::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF284OEA.mcool'... 2025-06-13 22:57:28,121::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-13 23:37:52,782::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF284OEA.mcool' in 0:40:24.725432. 2025-06-13 23:37:52,856::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF309UNV.mcool'... 2025-06-13 23:37:52,919::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 00:18:09,300::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF309UNV.mcool' in 0:40:16.443615. 2025-06-14 00:18:09,373::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF333WCK.mcool'... 2025-06-14 00:18:09,447::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 00:56:47,607::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF333WCK.mcool' in 0:38:38.233667. 2025-06-14 00:56:47,681::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF355NFJ.mcool'... 2025-06-14 00:56:47,790::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 01:37:36,163::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF355NFJ.mcool' in 0:40:48.481563. 2025-06-14 01:37:36,237::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF355VJW.mcool'... 2025-06-14 01:37:36,303::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 02:18:42,099::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF355VJW.mcool' in 0:41:05.862658. 2025-06-14 02:18:42,173::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF395INO.mcool'... 2025-06-14 02:18:42,255::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 03:01:05,126::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF395INO.mcool' in 0:42:22.952712. 2025-06-14 03:01:05,210::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF417GBZ.mcool'... 2025-06-14 03:01:05,277::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 03:41:34,979::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF417GBZ.mcool' in 0:40:29.768153. 2025-06-14 03:41:35,052::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF442IGJ.mcool'... 2025-06-14 03:41:35,118::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 04:22:55,547::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF442IGJ.mcool' in 0:41:20.494808. 2025-06-14 04:22:55,630::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF458VBB.mcool'... 2025-06-14 04:22:55,691::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 05:04:25,349::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF458VBB.mcool' in 0:41:29.718926. 2025-06-14 05:04:25,431::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF493SFI.mcool'... 2025-06-14 05:04:25,489::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 05:46:17,226::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF493SFI.mcool' in 0:41:51.794924. 2025-06-14 05:46:17,308::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF493YNC.mcool'... 2025-06-14 05:46:17,367::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 06:27:13,021::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF493YNC.mcool' in 0:40:55.712984. 2025-06-14 06:27:13,095::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF496GEU.mcool'... 2025-06-14 06:27:13,156::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 07:06:55,247::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF496GEU.mcool' in 0:39:42.152117. 2025-06-14 07:06:55,329::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF499BVX.mcool'... 2025-06-14 07:06:55,392::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 07:47:32,691::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF499BVX.mcool' in 0:40:37.361187. 2025-06-14 07:47:32,772::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF515ZBF.mcool'... 2025-06-14 07:47:32,840::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 08:28:26,253::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF515ZBF.mcool' in 0:40:53.480064. 2025-06-14 08:28:26,327::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF520GFL.mcool'... 2025-06-14 08:28:26,403::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 09:08:26,123::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF520GFL.mcool' in 0:39:59.796349. 2025-06-14 09:08:26,198::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF545GBW.mcool'... 2025-06-14 09:08:26,253::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 09:49:05,245::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF545GBW.mcool' in 0:40:39.047442. 2025-06-14 09:49:05,327::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF556RLR.mcool'... 2025-06-14 09:49:05,386::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 10:31:11,087::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF556RLR.mcool' in 0:42:05.759888. 2025-06-14 10:31:11,170::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF558DYU.mcool'... 2025-06-14 10:31:11,203::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 11:13:45,119::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF558DYU.mcool' in 0:42:33.948428. 2025-06-14 11:13:45,194::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF571GTF.mcool'... 2025-06-14 11:13:45,226::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 11:56:34,203::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF571GTF.mcool' in 0:42:49.009522. 2025-06-14 11:56:34,289::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF579CAR.mcool'... 2025-06-14 11:56:34,324::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 12:40:04,069::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF579CAR.mcool' in 0:43:29.779487. 2025-06-14 12:40:04,156::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF586MQY.mcool'... 2025-06-14 12:40:04,197::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 13:26:21,531::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF586MQY.mcool' in 0:46:17.375030. 2025-06-14 13:26:21,614::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF591MHA.mcool'... 2025-06-14 13:26:21,634::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 14:06:34,465::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF591MHA.mcool' in 0:40:12.851140. 2025-06-14 14:06:34,548::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF605CEN.mcool'... 2025-06-14 14:06:34,580::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 14:49:38,943::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF605CEN.mcool' in 0:43:04.394998. 2025-06-14 14:49:39,016::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF614IPZ.mcool'... 2025-06-14 14:49:39,045::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 15:31:15,887::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF614IPZ.mcool' in 0:41:36.871294. 2025-06-14 15:31:15,973::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF625VNK.mcool'... 2025-06-14 15:31:16,001::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 16:13:13,367::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF625VNK.mcool' in 0:41:57.394199. 2025-06-14 16:13:13,452::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF628LQQ.mcool'... 2025-06-14 16:13:13,513::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 16:57:13,166::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF628LQQ.mcool' in 0:43:59.713545. 2025-06-14 16:57:13,239::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF653HCO.mcool'... 2025-06-14 16:57:13,261::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 17:38:11,004::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF653HCO.mcool' in 0:40:57.764501. 2025-06-14 17:38:11,078::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF654YIQ.mcool'... 2025-06-14 17:38:11,304::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 18:22:39,170::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF654YIQ.mcool' in 0:44:28.091596. 2025-06-14 18:22:39,254::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF660JWA.mcool'... 2025-06-14 18:22:39,547::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 19:05:26,803::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF660JWA.mcool' in 0:42:47.549418. 2025-06-14 19:05:26,885::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF663FRL.mcool'... 2025-06-14 19:05:27,119::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 19:48:18,971::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF663FRL.mcool' in 0:42:52.085898. 2025-06-14 19:48:19,044::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF684YCT.mcool'... 2025-06-14 19:48:19,309::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 20:31:21,088::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF684YCT.mcool' in 0:43:02.043701. 2025-06-14 20:31:21,163::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF687ATD.mcool'... 2025-06-14 20:31:21,418::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 21:14:53,527::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF687ATD.mcool' in 0:43:32.364151. 2025-06-14 21:14:53,600::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF700CYI.mcool'... 2025-06-14 21:14:53,935::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 21:58:34,312::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF700CYI.mcool' in 0:43:40.711628. 2025-06-14 21:58:34,386::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF705YZH.mcool'... 2025-06-14 21:58:34,647::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 22:42:15,557::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF705YZH.mcool' in 0:43:41.170578. 2025-06-14 22:42:15,631::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF711XSR.mcool'... 2025-06-14 22:42:16,008::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-14 23:26:11,751::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF711XSR.mcool' in 0:43:56.119834. 2025-06-14 23:26:11,832::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF736ITL.mcool'... 2025-06-14 23:26:12,139::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 00:09:54,050::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF736ITL.mcool' in 0:43:42.218066. 2025-06-15 00:09:54,127::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF782WVZ.mcool'... 2025-06-15 00:09:54,459::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 00:53:36,584::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF782WVZ.mcool' in 0:43:42.456497. 2025-06-15 00:53:36,666::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF783KQI.mcool'... 2025-06-15 00:53:36,952::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 01:35:35,125::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF783KQI.mcool' in 0:41:58.458724. 2025-06-15 01:35:35,199::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF839VMS.mcool'... 2025-06-15 01:35:35,466::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 02:18:44,621::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF839VMS.mcool' in 0:43:09.421237. 2025-06-15 02:18:44,703::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF842DUO.mcool'... 2025-06-15 02:18:44,879::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 03:01:22,283::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF842DUO.mcool' in 0:42:37.579074. 2025-06-15 03:01:22,365::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF883XXW.mcool'... 2025-06-15 03:01:22,617::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 03:45:10,685::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF883XXW.mcool' in 0:43:48.319198. 2025-06-15 03:45:10,759::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF897KRI.mcool'... 2025-06-15 03:45:11,139::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 04:28:25,366::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF897KRI.mcool' in 0:43:14.607482. 2025-06-15 04:28:25,451::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF911AHQ.mcool'... 2025-06-15 04:28:25,739::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 05:11:57,273::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF911AHQ.mcool' in 0:43:31.821503. 2025-06-15 05:11:57,347::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF925QIF.mcool'... 2025-06-15 05:11:57,693::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 05:55:19,991::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF925QIF.mcool' in 0:43:22.643755. 2025-06-15 05:55:20,064::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF943JRY.mcool'... 2025-06-15 05:55:20,314::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 06:40:05,362::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF943JRY.mcool' in 0:44:45.297917. 2025-06-15 06:40:05,444::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF952JZV.mcool'... 2025-06-15 06:40:05,775::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 07:23:16,211::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF952JZV.mcool' in 0:43:10.767047. 2025-06-15 07:23:16,285::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF958DWQ.mcool'... 2025-06-15 07:23:16,595::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 08:06:35,179::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF958DWQ.mcool' in 0:43:18.893999. 2025-06-15 08:06:35,260::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF962EDB.mcool'... 2025-06-15 08:06:35,613::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 08:50:13,341::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF962EDB.mcool' in 0:43:38.081471. 2025-06-15 08:50:13,426::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF965BPU.mcool'... 2025-06-15 08:50:13,806::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 09:33:19,512::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF965BPU.mcool' in 0:43:06.085854. 2025-06-15 09:33:19,594::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ENCFF980NXK.mcool'... 2025-06-15 09:33:19,852::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 10:17:10,351::INFO::decompose_cooler_file: Finished decomposition for 'ENCFF980NXK.mcool' in 0:43:50.757077. 2025-06-15 10:17:10,426::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'ESC-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 10:17:10,602::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 11:00:16,647::INFO::decompose_cooler_file: Finished decomposition for 'ESC-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool' in 0:43:06.220925. 2025-06-15 11:00:16,721::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'HB-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 11:00:16,955::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 11:43:26,045::INFO::decompose_cooler_file: Finished decomposition for 'HB-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool' in 0:43:09.323940. 2025-06-15 11:43:26,130::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'hESC_pool.hg38.mapq_30.100.mcool'... 2025-06-15 11:43:26,655::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 12:27:58,486::INFO::decompose_cooler_file: Finished decomposition for 'hESC_pool.hg38.mapq_30.100.mcool' in 0:44:32.356182. 2025-06-15 12:27:58,568::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'iHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 12:27:59,125::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 13:11:32,682::INFO::decompose_cooler_file: Finished decomposition for 'iHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool' in 0:43:34.113970. 2025-06-15 13:11:32,766::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'mHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 13:11:33,231::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 13:54:50,262::INFO::decompose_cooler_file: Finished decomposition for 'mHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool' in 0:43:17.495283. 2025-06-15 13:54:50,339::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'PGT_pool.hg38.mapq_30.100.mcool'... 2025-06-15 13:54:50,534::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 14:37:48,999::INFO::decompose_cooler_file: Finished decomposition for 'PGT_pool.hg38.mapq_30.100.mcool' in 0:42:58.659942. 2025-06-15 14:37:49,072::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'PH_pool.hg38.mapq_30.100.mcool'... 2025-06-15 14:37:49,492::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 15:21:20,873::INFO::decompose_cooler_file: Finished decomposition for 'PH_pool.hg38.mapq_30.100.mcool' in 0:43:31.800550. 2025-06-15 15:21:20,949::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'PP_pool.hg38.mapq_30.100.mcool'... 2025-06-15 15:21:21,249::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 16:03:56,437::INFO::decompose_cooler_file: Finished decomposition for 'PP_pool.hg38.mapq_30.100.mcool' in 0:42:35.488050. 2025-06-15 16:03:56,520::INFO::decompose_cooler_file: Computing dimensionality reduction for input file: 'SC_Beta_pool.hg38.mapq_30.100.mcool'... 2025-06-15 16:03:57,063::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 16:46:52,200::INFO::decompose_cooler_file: Finished decomposition for 'SC_Beta_pool.hg38.mapq_30.100.mcool' in 0:42:55.680417. 2025-06-15 16:46:52,282::INFO::run: Model training complete. Training time: 3 days, 3:10:41.553424. 2025-06-15 16:46:52,282::INFO::run: Computing embeddings using fully trained model... 2025-06-15 16:46:52,282::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day00_ESC_pool.hg38.mapq_30.100.mcool'... 2025-06-15 16:46:52,490::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 16:50:49,051::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day02_mesoderm_pool.hg38.mapq_30.100.mcool'... 2025-06-15 16:50:49,214::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 16:55:02,954::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day05_cardiacMesoderm_pool.hg38.mapq_30.100.mcool'... 2025-06-15 16:55:03,142::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 16:59:08,089::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day07_cardiacProgenitor_pool.hg38.mapq_30.100.mcool'... 2025-06-15 16:59:08,314::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:03:33,192::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day15_primativeCardiomyocyte_pool.hg38.mapq_30.100.mcool'... 2025-06-15 17:03:33,341::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:07:19,621::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'day80_ventricularCardiomyocyte_pool.hg38.mapq_30.100.mcool'... 2025-06-15 17:07:19,796::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:11:07,037::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'DE-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 17:11:07,228::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:14:52,130::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'DE_pool.hg38.mapq_30.100.mcool'... 2025-06-15 17:14:52,306::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:18:12,431::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF004YZQ.mcool'... 2025-06-15 17:18:12,745::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:22:27,321::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF009ONH.mcool'... 2025-06-15 17:22:27,546::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:26:18,260::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF019YVI.mcool'... 2025-06-15 17:26:18,502::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:30:10,625::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF029UAL.mcool'... 2025-06-15 17:30:10,925::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:34:06,323::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF035BLF.mcool'... 2025-06-15 17:34:06,993::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:38:16,557::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF044TCQ.mcool'... 2025-06-15 17:38:16,809::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:42:19,277::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF059WMS.mcool'... 2025-06-15 17:42:19,426::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:46:28,288::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF076LWH.mcool'... 2025-06-15 17:46:28,546::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:50:50,210::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF081PMO.mcool'... 2025-06-15 17:50:50,500::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 17:55:48,367::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF094KKX.mcool'... 2025-06-15 17:55:49,025::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:00:03,780::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF136XCV.mcool'... 2025-06-15 18:00:04,195::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:03:38,054::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF140ROU.mcool'... 2025-06-15 18:03:38,267::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:07:31,089::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF149IHN.mcool'... 2025-06-15 18:07:31,283::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:11:07,439::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF176LIZ.mcool'... 2025-06-15 18:11:07,740::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:15:13,802::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF185AYZ.mcool'... 2025-06-15 18:15:14,055::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:19:19,341::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF193CQL.mcool'... 2025-06-15 18:19:19,787::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 18:23:24,736::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF197OWW.mcool'... 2025-06-15 18:23:24,962::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 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'ENCFF943JRY.mcool'... 2025-06-15 21:50:53,590::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 21:55:12,502::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF952JZV.mcool'... 2025-06-15 21:55:12,668::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 21:59:21,900::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF958DWQ.mcool'... 2025-06-15 21:59:22,054::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:01:41,102::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF962EDB.mcool'... 2025-06-15 22:01:41,183::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:05:46,508::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF965BPU.mcool'... 2025-06-15 22:05:46,623::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:10:19,334::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ENCFF980NXK.mcool'... 2025-06-15 22:10:19,481::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:14:49,024::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'ESC-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 22:14:49,130::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:18:18,604::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'HB-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 22:18:18,774::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:20:49,519::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'hESC_pool.hg38.mapq_30.100.mcool'... 2025-06-15 22:20:49,873::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:23:58,319::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'iHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 22:23:58,460::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:27:32,154::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'mHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool'... 2025-06-15 22:27:32,274::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:31:29,886::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'PGT_pool.hg38.mapq_30.100.mcool'... 2025-06-15 22:31:29,987::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:34:47,017::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'PH_pool.hg38.mapq_30.100.mcool'... 2025-06-15 22:34:47,071::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:37:08,121::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'PP_pool.hg38.mapq_30.100.mcool'... 2025-06-15 22:37:08,169::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:40:38,853::INFO::compute_output_embeddings_single_file: Computing embeddings for input file: 'SC_Beta_pool.hg38.mapq_30.100.mcool'... 2025-06-15 22:40:38,943::INFO::preprocess_matrix: Loading preprocessed matrix from disk... 2025-06-15 22:44:09,024::INFO::run: Saving results... 2025-06-15 22:44:09,586::INFO::save_model: Saved model to 'output_2025_06_12_13_36_PCA-32_50000bp_hg38_model.pkl.gz' in 0:00:00.561111. 2025-06-15 22:56:32,695::INFO::run: Saved embeddings to 'output_2025_06_12_13_36_PCA-32_50000bp_hg38_embeddings.csv.gz' and 'output_2025_06_12_13_36_PCA-32_50000bp_hg38_embeddings.pq'. 2025-06-15 22:56:32,708::INFO::run: Finished joint PCA in 3 days, 9:20:21.979515. 2025-06-15 22:56:34,936::INFO::__init__: PostProcessor :: configuration: ==================== Post Processor Configuration ==================== parquet_file : output_2025_06_12_13_36_PCA-32_50000bp_hg38_embeddings.pq output : output_2025_06_12_13_36_PCA-32_50000bp_hg38 umap_neighbours : [30, 100, 500] kmeans_clusters : [5, 6, 7, 8, 9, 10, 15, 20] leiden_resolutions : [0.1, 0.2, 0.3, 0.5, 0.8, 1.0] method : PCA log_level : INFO ======================================================================== 2025-06-15 22:56:35,527::INFO::run: Running post-processing 2025-06-15 22:56:44,156::INFO::normalize_embeddings: Normalizing embeddings for DE-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool 2025-06-15 22:56:51,482::INFO::normalize_embeddings: Normalizing embeddings for DE_pool.hg38.mapq_30.100.mcool 2025-06-15 22:56:57,094::INFO::normalize_embeddings: Normalizing embeddings for ENCFF004YZQ.mcool 2025-06-15 22:57:00,712::INFO::normalize_embeddings: Normalizing embeddings for ENCFF009ONH.mcool 2025-06-15 22:57:03,784::INFO::normalize_embeddings: Normalizing 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22:59:10,851::INFO::normalize_embeddings: Normalizing embeddings for ENCFF687ATD.mcool 2025-06-15 22:59:13,437::INFO::normalize_embeddings: Normalizing embeddings for ENCFF700CYI.mcool 2025-06-15 22:59:16,029::INFO::normalize_embeddings: Normalizing embeddings for ENCFF705YZH.mcool 2025-06-15 22:59:18,661::INFO::normalize_embeddings: Normalizing embeddings for ENCFF711XSR.mcool 2025-06-15 22:59:21,301::INFO::normalize_embeddings: Normalizing embeddings for ENCFF736ITL.mcool 2025-06-15 22:59:23,870::INFO::normalize_embeddings: Normalizing embeddings for ENCFF782WVZ.mcool 2025-06-15 22:59:26,440::INFO::normalize_embeddings: Normalizing embeddings for ENCFF783KQI.mcool 2025-06-15 22:59:29,041::INFO::normalize_embeddings: Normalizing embeddings for ENCFF839VMS.mcool 2025-06-15 22:59:31,654::INFO::normalize_embeddings: Normalizing embeddings for ENCFF842DUO.mcool 2025-06-15 22:59:34,247::INFO::normalize_embeddings: Normalizing embeddings for ENCFF883XXW.mcool 2025-06-15 22:59:36,845::INFO::normalize_embeddings: Normalizing embeddings for ENCFF897KRI.mcool 2025-06-15 22:59:39,452::INFO::normalize_embeddings: Normalizing embeddings for ENCFF911AHQ.mcool 2025-06-15 22:59:42,078::INFO::normalize_embeddings: Normalizing embeddings for ENCFF925QIF.mcool 2025-06-15 22:59:44,688::INFO::normalize_embeddings: Normalizing embeddings for ENCFF943JRY.mcool 2025-06-15 22:59:47,308::INFO::normalize_embeddings: Normalizing embeddings for ENCFF952JZV.mcool 2025-06-15 22:59:49,935::INFO::normalize_embeddings: Normalizing embeddings for ENCFF958DWQ.mcool 2025-06-15 22:59:52,574::INFO::normalize_embeddings: Normalizing embeddings for ENCFF962EDB.mcool 2025-06-15 22:59:55,249::INFO::normalize_embeddings: Normalizing embeddings for ENCFF965BPU.mcool 2025-06-15 22:59:57,957::INFO::normalize_embeddings: Normalizing embeddings for ENCFF980NXK.mcool 2025-06-15 23:00:00,654::INFO::normalize_embeddings: Normalizing embeddings for ESC-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool 2025-06-15 23:00:03,259::INFO::normalize_embeddings: Normalizing embeddings for HB-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool 2025-06-15 23:00:05,871::INFO::normalize_embeddings: Normalizing embeddings for PGT_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:08,560::INFO::normalize_embeddings: Normalizing embeddings for PH_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:11,240::INFO::normalize_embeddings: Normalizing embeddings for PP_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:13,927::INFO::normalize_embeddings: Normalizing embeddings for SC_Beta_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:16,616::INFO::normalize_embeddings: Normalizing embeddings for day00_ESC_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:18,819::INFO::normalize_embeddings: Normalizing embeddings for day02_mesoderm_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:21,020::INFO::normalize_embeddings: Normalizing embeddings for day05_cardiacMesoderm_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:23,230::INFO::normalize_embeddings: Normalizing embeddings for day07_cardiacProgenitor_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:25,455::INFO::normalize_embeddings: Normalizing embeddings for day15_primativeCardiomyocyte_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:27,682::INFO::normalize_embeddings: Normalizing embeddings for day80_ventricularCardiomyocyte_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:29,904::INFO::normalize_embeddings: Normalizing embeddings for hESC_pool.hg38.mapq_30.100.mcool 2025-06-15 23:00:32,502::INFO::normalize_embeddings: Normalizing embeddings for iHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool 2025-06-15 23:00:35,109::INFO::normalize_embeddings: Normalizing embeddings for mHEP-FA-DSG-DdeI-DpnII-P1P2.hg38.mapq_30.1000.mcool 2025-06-15 23:00:45,310::INFO::run: Components shape: (4493165, 32) 2025-06-15 23:00:45,311::INFO::run_kmeans: Running KMeans clustering with 5 clusters 2025-06-15 23:01:06,223::INFO::run_kmeans: Running KMeans clustering with 6 clusters 2025-06-15 23:01:32,417::INFO::run_kmeans: Running KMeans clustering with 7 clusters 2025-06-15 23:02:07,403::INFO::run_kmeans: Running KMeans clustering with 8 clusters 2025-06-15 23:02:39,953::INFO::run_kmeans: Running KMeans clustering with 9 clusters 2025-06-15 23:03:15,114::INFO::run_kmeans: Running KMeans clustering with 10 clusters 2025-06-15 23:03:52,815::INFO::run_kmeans: Running KMeans clustering with 15 clusters 2025-06-15 23:05:23,450::INFO::run_kmeans: Running KMeans clustering with 20 clusters 2025-06-15 23:06:30,057::INFO::run_leiden: Running Leiden clustering with 500 neighbors.