section analysis data command tool version variant group threads run order cpu_s user_s system_s wall_s peak_mb started processor cores memory_gb system node python chromosomix command_line 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb insulation chromosomix 0.19.0 at 997e59c 1 1 0 4.883029 4.394012 0.489017 3.9514228879997972 294.52734375 2026-11-01T23:22:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --window 10 --out insulation/app 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb cooltools-insulation cooltools 0.7.1 4 1 1 12.045837 11.147197 0.89864 6.114058606999606 874.759765625 2026-11-01T23:22:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 insulation/cooltools.tsv 4 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb di chromosomix 0.19.0 at 997e59c 1 1 2 2.355821 2.201607 0.154214 1.837029541999982 211.578125 2026-11-01T23:22:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix di data/4DNFIOZ1TRUS.mcool::/resolutions/50000 --window 40 --out di/app 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb domaincaller-di domaincaller 0.1.0 1 1 3 2.783527 2.614566 0.168961 2.479453480000302 258.30859375 2026-11-01T23:22:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/domaincaller_di.py data/4DNFIOZ1TRUS.mcool::/resolutions/50000 di/domaincaller.npy 3 Compartments mouse Hi-C, 100 kb, GC-phased compartments chromosomix 0.19.0 at 997e59c 1 1 4 6.473048 6.093286 0.379762 4.714204427999903 287.45703125 2026-11-01T23:23:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix compartments data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --components 3 --phaseTrack compartments/gc.bedGraph --out compartments/app 3 Compartments mouse Hi-C, 100 kb, GC-phased cooltools-eigs cooltools 0.7.1 1 1 5 15.057006 14.533076 0.52393 8.139823864000391 559.1015625 2026-11-01T23:23:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_eigs_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 compartments/gc.tsv compartments/cooltools 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-yeast chromosomix 0.19.0 at 997e59c yeast 800 bp yeast 800 bp 1 1 6 0.7302139999999999 0.621737 0.10847699999999999 0.5467870640004548 211.578125 2026-11-01T23:23:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/GSE151553_A364_merged.mcool::/resolutions/800 --quantity expected --scope file --out ps/yeast 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-mouse chromosomix 0.19.0 at 997e59c mouse 10 kb mouse 10 kb 1 1 7 2.841714 2.538357 0.303357 2.361191033999603 235.00390625 2026-11-01T23:23:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --quantity expected --scope file --out ps/mouse 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-yeast cooltools 0.7.1 yeast 800 bp yeast 800 bp 4 1 8 3.164059 2.676891 0.487168 2.513188218000323 957.79296875 2026-11-01T23:23:17 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/GSE151553_A364_merged.mcool::/resolutions/800 ps/yeast-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-mouse cooltools 0.7.1 mouse 10 kb mouse 10 kb 4 1 9 22.739475 16.710867 6.028608 8.354057980999642 10618.9384765625 2026-11-01T23:23:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 ps/mouse-cooltools.tsv 4 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 peaks chromosomix 0.19.0 at 997e59c 1 1 10 20.322116 18.640153 1.681963 18.48283301599986 264.6796875 2026-11-01T23:23:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/4DNFIIY4QW2D.chr19.bw --replicate data/4DNFITBRHVZE.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out yapc/app 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 seed 0 seed 0 1 1 11 61.676931 58.205922 3.471009 61.92214430399963 1667.703125 2026-11-01T23:23:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 yapc/seed0/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosomix 0.19.0 at 997e59c 1 1 12 6.119581 5.910571 0.20901 5.024923895999564 270.46484375 2026-11-01T23:24:48 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix chromosight data/GSE151553_A364_merged.mcool::/resolutions/800 --pattern loops --out loops/app 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosight 1.6.3 4 1 13 30.345978000000002 28.978677 1.3673009999999999 10.339175101000365 767.8955078125 2026-11-01T23:24:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight detect --pattern loops --threads 4 data/GSE151553_A364_merged.mcool::/resolutions/800 loops/chromosight/loops 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep chromosomix 0.19.0 at 997e59c 3 maps, 3 pairs 3 maps, 3 pairs 1 1 14 4.01583 3.730207 0.28562299999999996 3.2479040019998138 262.03125 2026-11-01T23:25:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix hicrep data/4DNFIH8L6WON.mcool::/resolutions/100000 --against data/4DNFITBCUX56.mcool::/resolutions/100000 --against data/4DNFIIML46E5.mcool::/resolutions/100000 --maxDistance 50 --smooth 1 --no-balance --sequences chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ --out hicrep/app 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep hicrep 0.2.6 3 maps, 3 pairs 3 maps, 3 pairs 1 1 15 5.390556 5.184575 0.205981 5.095090961000096 258.0546875 2026-11-01T23:25:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/hicrep_scc.py hicrep/hicrep.tsv chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ 4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000 4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000 4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads reconstruct3d-seed0 chromosomix 0.19.0 at 997e59c seed 0 seed 0 1 1 16 5.740171 5.589009 0.151162 5.43776054799946 211.578125 2026-11-01T23:25:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 0 --out pastis/app-seed0 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads pastis-seed0 pastis 0.5.0 seed 0 seed 0 1 1 17 78.33771200000001 75.066647 3.271065 29.09764838599949 359.40234375 2026-11-01T23:25:17 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed0.npy 0 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-raw chromosomix 0.19.0 at 997e59c raw raw 1 1 18 3.828213 3.482849 0.345364 3.1120616129992413 303.453125 2026-11-01T23:25:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --out coverage/raw 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 1 19 4.082525 3.626125 0.4564 3.393615516999489 276.40234375 2026-11-01T23:25:49 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --balance --out coverage/balanced 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-raw cooltools 0.7.1 raw raw 4 1 20 5.6625190000000005 4.901912 0.7606069999999999 2.5661059879994355 1486.1728515625 2026-11-01T23:25:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-raw.tsv 4 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-balanced cooltools 0.7.1 balanced balanced 4 1 21 6.277718999999999 5.510483 0.7672359999999999 3.055554698999913 1669.2568359375 2026-11-01T23:25:55 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-balanced.tsv 4 weight 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome fourc-Sox2 chromosomix 0.19.0 at 997e59c Sox2 Sox2 1 1 22 1.4157039999999999 1.21274 0.20296399999999998 1.0816786979994504 276.57421875 2026-11-01T23:25:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr3:34,650,001-34,660,000 --no-cis --out virtual4c/Sox2 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome cooltools-virtual4c-Sox2 cooltools 0.7.1 Sox2 Sox2 4 1 23 6.677084 6.136125 0.540959 2.807817731999421 539.1240234375 2026-11-01T23:25:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr3:34650000-34660000 virtual4c/cooltools-Sox2.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw chromosomix 0.19.0 at 997e59c raw raw 1 1 24 1.3434899999999999 1.226146 0.11734399999999999 0.9134469690006881 211.578125 2026-11-01T23:26:02 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/raw 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw-every chromosomix 0.19.0 at 997e59c raw, every loop raw, every loop 1 1 25 2.058941 1.895708 0.163233 1.4694493920005698 211.578125 2026-11-01T23:26:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/raw-every 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-local chromosomix 0.19.0 at 997e59c on the diagonal, raw on the diagonal, raw 1 1 26 2.204478 2.026145 0.178333 1.5758367570006158 214.671875 2026-11-01T23:26:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm none --mode fixed --window 5 --minDiag 2 --out apa/local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-controls-seed1 chromosomix 0.19.0 at 997e59c controls, seed 1 controls 1 1 27 2.364514 2.1946149999999998 0.169899 1.7053033120000691 211.578125 2026-11-01T23:26:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 1 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed1 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw coolpuppy 1.1.0 raw raw 4 1 28 8.658007 7.745186 0.912821 3.3869032620004873 811.3408203125 2026-11-01T23:26:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw-every coolpuppy 1.1.0 raw, every loop raw, every loop 4 1 29 9.009391 8.080989 0.928402 3.6434772210004667 894.755859375 2026-11-01T23:26:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw-every.tsv 4 --mindist 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-local coolpuppy 1.1.0 on the diagonal, raw on the diagonal, raw 4 1 30 9.285789 8.357928 0.9278609999999999 3.6912912790003247 1023.1123046875 2026-11-01T23:26:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local.tsv 4 --local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-controls-seed0 coolpuppy 1.1.0 controls, seed 0 controls 4 1 31 8.627373 7.73302 0.894353 3.387161161000222 882.5322265625 2026-11-01T23:26:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed0.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 0 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops apa-chromosight chromosomix 0.19.0 at 997e59c 1 1 32 5.0249429999999995 4.807562 0.217381 3.7240411419998054 240.51171875 2026-11-01T23:26:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm chromosight --out chromosight-quantify/app 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops chromosight-quantify chromosight 1.6.3 4 1 33 83.64723000000001 80.16535 3.48188 26.710915722999744 1470.703125 2026-11-01T23:26:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight quantify --pattern loops --threads 4 apa/loops.bedpe data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chromosight-quantify/quantify 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boost-chr1 chromosomix 0.19.0 at 997e59c chr1, 1,955 bins chr1, 1,955 bins 1 1 34 3.1891570000000002 2.78065 0.408507 2.982326497000031 639.02734375 2026-11-01T23:26:52 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr1 --out boost-hic/chr1 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boosthic-chr1 Boost-HiC a615aff chr1, 1,955 bins chr1, 1,955 bins 1 1 35 20.079527 19.850414999999998 0.22911199999999998 19.56036451699947 462.5 2026-11-01T23:26:55 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr1 boost-hic/boosthic-chr1 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot chromosomix 0.19.0 at 997e59c TSS 1 1 36 4.217244 3.540582 0.676662 3.8076962899995124 384.3671875 2026-11-01T23:27:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot-two chromosomix 0.19.0 at 997e59c TSS, two tracks 1 1 37 7.436645 6.262113 1.174532 6.339177206999921 430.625 2026-11-01T23:27:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --tracks data/4DNFITBRHVZE.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app-two 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix deepTools 4.0.0 computeMatrix TSS 4 1 38 3.3501659999999998 2.9664289999999998 0.383737 3.2462142410004162 211.578125 2026-11-01T23:27:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile deepTools 4.0.0 plotProfile TSS 1 1 39 1.830916 1.734868 0.096048 1.5513540209994972 219.3203125 2026-11-01T23:27:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools.mat.gz -out metaplot/deeptools-profile.png --outFileNameData metaplot/deeptools-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix-two deepTools 4.0.0 computeMatrix TSS, two tracks 4 1 40 6.254423 5.658526 0.595897 3.9068754230002014 244.828125 2026-11-01T23:27:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw data/4DNFITBRHVZE.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools-two.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile-two deepTools 4.0.0 plotProfile TSS, two tracks 1 1 41 2.5195469999999998 2.3986169999999998 0.12093 2.214148708999346 262.328125 2026-11-01T23:27:34 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-profile.png --outFileNameData metaplot/deeptools-two-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotheatmap-two deepTools 4.0.0 plotHeatmap TSS, two tracks 1 1 42 3.1927339999999997 2.975685 0.217049 2.8867575919994124 484.5234375 2026-11-01T23:27:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-heatmap.png --outFileSortedRegions metaplot/deeptools-two-heatmap.bed 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 overlap chromosomix 0.19.0 at 997e59c 1 1 43 1.094429 1.057617 0.036812 1.0156890839998596 211.578125 2026-11-01T23:27:39 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix overlap --sequence data/mm10.fa --features yapc/seed0/yapc_0.05.bed --features overlap/promoters.bed --a yapc/seed0/yapc_0.05.bed --b overlap/promoters.bed --shuffle --iterations 1000 --seed 1 --out overlap/app 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 bedtools-overlap bedtools 2.31.1 1 1 44 42.116771 28.616869 13.499902 37.77399356699971 211.578125 2026-11-01T23:27:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bedtools_overlap.py yapc/seed0/yapc_0.05.bed overlap/promoters.bed overlap/mm10.genome 1000 overlap/bedtools 16 Base composition mm10, 10 kb bins composition chromosomix 0.19.0 at 997e59c 1 1 45 3.728611 3.032861 0.69575 7.593019138999807 245.34375 2026-11-01T23:28:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix composition --sequence data/mm10.fa --resolution 10000 --out composition/app 16 Base composition mm10, 10 kb bins composition bioframe, Biopython 0.8.0, 1.88 1 1 46 39.607603999999995 33.259828 6.347776 39.305620017000365 507.5390625 2026-11-01T23:28:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/composition.py data/mm10.fa 10000 composition/reference.tsv 17 Motif search mm10 chr19, two motifs, both strands motif-TGACTCA chromosomix 0.19.0 at 997e59c TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 1 1 47 5.174526 2.5716229999999998 2.602903 5.195177593000153 359.79296875 2026-11-01T23:29:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern TGACTCA --mismatches 1 --out motif/TGACTCA 17 Motif search mm10 chr19, two motifs, both strands motif-WGATAR chromosomix 0.19.0 at 997e59c WGATAR WGATAR 1 1 48 4.008129 2.150347 1.8577819999999998 3.9600083239993182 300.53125 2026-11-01T23:29:10 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern WGATAR --mismatches 0 --out motif/WGATAR 17 Motif search mm10 chr19, two motifs, both strands seqkit-TGACTCA seqkit 2.3.0 TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 4 1 49 17.905105 16.221109 1.683996 17.763620391000586 4118.73828125 2026-11-01T23:29:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -m 1 -p TGACTCA --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-TGACTCA.bed 17 Motif search mm10 chr19, two motifs, both strands seqkit-WGATAR seqkit 2.3.0 WGATAR WGATAR 4 1 50 6.265567 6.07573 0.18983699999999998 5.9844234909996885 342.9296875 2026-11-01T23:29:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -d -p WGATAR --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-WGATAR.bed 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-pearson chromosomix 0.19.0 at 997e59c 100 bp, pearson 100 bp windows 1 1 51 0.76527 0.666461 0.098809 0.5640465460000996 211.578125 2026-11-01T23:29:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method pearson --out trackcorr/app-100-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-spearman chromosomix 0.19.0 at 997e59c 100 bp, spearman 100 bp windows 1 1 52 1.53816 1.3506529999999999 0.18750699999999998 1.312383466999563 313.3046875 2026-11-01T23:29:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method spearman --out trackcorr/app-100-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-pearson chromosomix 0.19.0 at 997e59c 1,000 bp, pearson 1,000 bp windows 1 1 53 0.7350399999999999 0.652052 0.08298799999999999 0.5201225379996686 211.578125 2026-11-01T23:29:39 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method pearson --out trackcorr/app-1000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-spearman chromosomix 0.19.0 at 997e59c 1,000 bp, spearman 1,000 bp windows 1 1 54 0.8203189999999999 0.7436349999999999 0.076684 0.5694688379999207 211.578125 2026-11-01T23:29:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method spearman --out trackcorr/app-1000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-pearson chromosomix 0.19.0 at 997e59c 10,000 bp, pearson 10,000 bp windows 1 1 55 0.694724 0.62029 0.074434 0.486190171999624 211.578125 2026-11-01T23:29:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method pearson --out trackcorr/app-10000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-spearman chromosomix 0.19.0 at 997e59c 10,000 bp, spearman 10,000 bp windows 1 1 56 0.7138669999999999 0.635882 0.077985 0.49390220399982354 211.578125 2026-11-01T23:29:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method spearman --out trackcorr/app-10000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-100 deepTools 4.0.0 100 bp, the windows 100 bp windows 4 1 57 187.849761 183.365842 4.483919 49.45382938000057 305.294921875 2026-11-01T23:29:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 100 -p 4 -o trackcorr/deeptools-100.npz --outRawCounts trackcorr/deeptools-100.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-pearson deepTools 4.0.0 100 bp, pearson 100 bp windows 1 1 58 1.6838499999999998 1.538468 0.14538199999999998 1.0733127189996594 270.546875 2026-11-01T23:30:31 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c pearson -p heatmap -o trackcorr/deeptools-100-pearson.png --outFileCorMatrix trackcorr/deeptools-100-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-spearman deepTools 4.0.0 100 bp, spearman 100 bp windows 1 1 59 2.1277179999999998 1.98467 0.14304799999999998 1.5102151020000747 269.92578125 2026-11-01T23:30:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c spearman -p heatmap -o trackcorr/deeptools-100-spearman.png --outFileCorMatrix trackcorr/deeptools-100-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-1000 deepTools 4.0.0 1,000 bp, the windows 1,000 bp windows 4 1 60 17.714942999999998 17.191052 0.523891 4.745449668999754 211.578125 2026-11-01T23:30:34 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 1000 -p 4 -o trackcorr/deeptools-1000.npz --outRawCounts trackcorr/deeptools-1000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-pearson deepTools 4.0.0 1,000 bp, pearson 1,000 bp windows 1 1 61 1.441374 1.344484 0.09688999999999999 0.8230731560006461 211.578125 2026-11-01T23:30:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c pearson -p heatmap -o trackcorr/deeptools-1000-pearson.png --outFileCorMatrix trackcorr/deeptools-1000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-spearman deepTools 4.0.0 1,000 bp, spearman 1,000 bp windows 1 1 62 1.436401 1.341639 0.094762 0.8164420250004696 211.578125 2026-11-01T23:30:39 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c spearman -p heatmap -o trackcorr/deeptools-1000-spearman.png --outFileCorMatrix trackcorr/deeptools-1000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-10000 deepTools 4.0.0 10,000 bp, the windows 10,000 bp windows 4 1 63 2.27827 2.162159 0.11611099999999999 0.7039426230003301 211.578125 2026-11-01T23:30:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 10000 -p 4 -o trackcorr/deeptools-10000.npz --outRawCounts trackcorr/deeptools-10000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-pearson deepTools 4.0.0 10,000 bp, pearson 10,000 bp windows 1 1 64 1.3855119999999999 1.3006039999999999 0.084908 0.7696901490007804 211.578125 2026-11-01T23:30:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c pearson -p heatmap -o trackcorr/deeptools-10000-pearson.png --outFileCorMatrix trackcorr/deeptools-10000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-spearman deepTools 4.0.0 10,000 bp, spearman 10,000 bp windows 1 1 65 1.365649 1.277672 0.087977 0.7473431600001277 211.578125 2026-11-01T23:30:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c spearman -p heatmap -o trackcorr/deeptools-10000-spearman.png --outFileCorMatrix trackcorr/deeptools-10000-spearman.tab 19 Loop calling mouse Hi-C, 10 kb, every chromosome loops chromosomix 0.19.0 at 997e59c 1 1 66 25.740306 24.338294 1.402012 22.209751042999414 470.83203125 2026-11-01T23:30:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix loops data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --out loopcalling/app 19 Loop calling mouse Hi-C, 10 kb, every chromosome cooltools-dots cooltools 0.7.1 4 1 67 560.587988 531.585744 29.002244 157.1747465620001 11530.779296875 2026-11-01T23:31:04 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_dots.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 loopcalling/cooltools.tsv 4 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches groupsignal-entries chromosomix 0.19.0 at 997e59c one value per entry one value per entry 1 1 68 0.661836 0.581125 0.08071099999999999 0.4619368730000133 211.578125 2026-11-01T23:33:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --out groupsignal/app-entries 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches pybigwig-groupsignal-entries pyBigWig, SciPy 0.3.26, 1.16.3 one value per entry one value per entry 1 1 69 1.545712 1.441799 0.10391299999999999 0.9271154110001589 211.578125 2026-11-01T23:33:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 0 groupsignal/reference-entries data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-insulation chromosomix 0.19.0 at 997e59c insulation, four scales insulation 1 1 70 1.3523800000000001 1.211653 0.140727 0.9984770529999878 216.91796875 2026-11-01T23:33:43 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIXP4QG5B_10000.chr19.cool --window 5 --scales 4 --out gm12878/insulation/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-peaks chromosomix 0.19.0 at 997e59c peaks peaks 1 1 71 40.293858 38.668431 1.625427 37.69367049700031 265.69140625 2026-11-01T23:33:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/ENCFF734CUT.chr19.bw --replicate data/ENCFF644EEX.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out gm12878/yapc/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw chromosomix 0.19.0 at 997e59c APA, raw APA 1 1 72 0.7564819999999999 0.6602939999999999 0.096188 0.525775851000617 211.578125 2026-11-01T23:34:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw-every chromosomix 0.19.0 at 997e59c APA, raw, every pair APA 1 1 73 1.201953 1.064818 0.137135 0.8572894489998362 211.578125 2026-11-01T23:34:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw-every 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-signal chromosomix 0.19.0 at 997e59c metaplot, CTCF and ATAC-seq, ±2 kb metaplot, signal 1 1 74 1.263917 1.062423 0.20149399999999998 0.9439205050002784 267.65234375 2026-11-01T23:34:23 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/ENCFF734CUT.chr19.bw --tracks data/ENCFF644EEX.chr19.bw --tracks data/ENCFF487LOB.chr19.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 2000 --step 50 --band none --out gm12878/metaplot/app-signal 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-insulation chromosomix 0.19.0 at 997e59c metaplot, insulation at four scales, ±500 kb metaplot, insulation 1 1 75 1.236631 1.034669 0.201962 0.9998382620005941 211.578125 2026-11-01T23:34:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 500000 --step 10000 --band none --out gm12878/metaplot/app-insulation 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-cooltools-insulation cooltools 0.7.1 insulation, four scales insulation 4 1 76 6.043152999999999 5.503906 0.5392469999999999 5.394619333000264 801.2177734375 2026-11-01T23:34:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation_scales.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/insulation/cooltools.tsv 4 50000 100000 200000 400000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 peaks, seed 0 peaks 1 1 77 80.079407 76.863833 3.215574 80.05650878400047 1596.828125 2026-11-01T23:34:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 gm12878/yapc/seed0/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw coolpuppy 1.1.0 APA, raw APA 4 1 78 3.243644 2.709426 0.534218 2.7924609739993684 1089.71875 2026-11-01T23:35:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw.tsv 4 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw-every coolpuppy 1.1.0 APA, raw, every pair APA 4 1 79 3.476844 3.00319 0.47365399999999996 2.991282290999152 1092.65625 2026-11-01T23:35:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw-every.tsv 4 --mindist 0 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-signal deepTools 4.0.0 computeMatrix metaplot, signal 4 1 80 0.793806 0.742883 0.050922999999999996 0.39014796699939325 211.578125 2026-11-01T23:35:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw data/ENCFF487LOB.chr19.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 2000 -a 2000 --binSize 50 -p 4 -o gm12878/metaplot/deeptools-signal.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-signal deepTools 4.0.0 plotProfile metaplot, signal 1 1 81 1.006906 0.949912 0.056993999999999996 0.6999676239993278 211.578125 2026-11-01T23:35:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-profile.png --outFileNameData gm12878/metaplot/deeptools-signal-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-signal deepTools 4.0.0 plotHeatmap metaplot, signal 1 1 82 1.423165 1.327154 0.096011 1.1142608629997994 211.578125 2026-11-01T23:35:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-signal-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-insulation deepTools 4.0.0 computeMatrix metaplot, insulation 4 1 83 39.611692 30.360747 9.250945 11.160873668000022 945.70703125 2026-11-01T23:35:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 500000 -a 500000 --binSize 10000 -p 4 -o gm12878/metaplot/deeptools-insulation.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-insulation deepTools 4.0.0 plotProfile metaplot, insulation 1 1 84 1.133686 1.0725959999999999 0.06109 0.8259657439994044 211.578125 2026-11-01T23:36:10 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-profile.png --outFileNameData gm12878/metaplot/deeptools-insulation-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-insulation deepTools 4.0.0 plotHeatmap metaplot, insulation 1 1 85 1.677633 1.582824 0.09480899999999999 1.3694553000004817 211.578125 2026-11-01T23:36:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-insulation-heatmap.bed 25 Pairs statistics yeast Hi-C contact list, deduplicated pairstats chromosomix 0.19.0 at 997e59c 1 1 86 67.685424 45.955571 21.729853 61.980999434000296 219.171875 2026-11-01T23:36:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix stats data/CH128.pairs.gz --out pairstats/app 25 Pairs statistics yeast Hi-C contact list, deduplicated pairtools-stats pairtools 1.1.2 1 1 87 86.805845 77.365441 9.440404 77.39063628399981 307.17578125 2026-11-01T23:37:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins restriction chromosomix 0.19.0 at 997e59c 1 1 88 1.058411 0.567045 0.49136599999999997 0.9684267739994539 211.578125 2026-11-01T23:38:31 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix restriction restriction/CH128.5000.cool --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-sites 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins bioframe-digest bioframe, Biopython 0.8.0, 1.88 1 1 89 1.120112 1.041175 0.078937 0.8141707700006009 211.578125 2026-11-01T23:38:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bioframe_digest.py data/R64-1-1.fa DpnII 5000 restriction/digest -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc chromosomix 0.19.0 at 997e59c 1 1 90 137.481089 94.94291 42.538179 122.80717193500004 330.15625 2026-11-01T23:38:33 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix pairsqc data/CH128.pairs.gz --bin-size 5000 --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-pairsqc 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooler-cload cooler 0.10.4 1 1 91 42.633548 41.661645 0.971903 42.389122032999694 2360.6875 2026-11-01T23:40:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 data/R64-1-1.chrom.sizes:5000 data/CH128.pairs.gz restriction/CH128.5000.cool 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-top pairtools 1.1.2 1 1 92 332.41079 322.981687 9.429103 201.58307638900078 211.578125 2026-11-01T23:41:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags.bed data/CH128.pairs.gz -o restriction/CH128.restricted.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-bottom pairtools 1.1.2 1 1 93 332.30149800000004 322.965774 9.335724 201.4401653999994 211.578125 2026-11-01T23:44:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags-bottom.bed data/CH128.pairs.gz -o restriction/CH128.restricted-bottom.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb restriction-reference pandas 2.3.3 1 1 94 75.41307599999999 73.313824 2.099252 78.22290676100056 862.66796875 2026-11-01T23:48:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/restriction_reference.py data/R64-1-1.fa DpnII restriction/CH128.restricted.pairs.gz restriction/CH128.restricted-bottom.pairs.gz restriction/pairtools -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooltools-coverage-sites cooltools 0.7.1 4 1 95 2.0417929999999997 1.7719019999999999 0.269891 1.3996465130003344 296.42578125 2026-11-01T23:49:20 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage_sites.py restriction/CH128.5000.cool restriction/digest.sites.tsv restriction/coverage 4 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc-pairtools-stats pairtools 1.1.2 1 1 96 82.690648 73.26684 9.423808 73.026801299 309.890625 2026-11-01T23:49:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-raw chromosomix 0.19.0 at 997e59c raw raw 1 1 97 5.806078 5.282629 0.5234489999999999 6.099122559999159 537.5703125 2026-11-01T23:50:34 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --no-balance --out arrowhead/app-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 1 98 6.197794 5.509373 0.688421 6.176297214999067 530.1328125 2026-11-01T23:50:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --out arrowhead/app-balanced 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-raw Juicer Tools 1.22.01, on Java 21.0.13 raw raw 1 1 99 40.708438 36.656137 4.052301 20.44912360499984 2875.15625 2026-11-01T23:50:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k NONE --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-balanced Juicer Tools 1.22.01, on Java 21.0.13 balanced balanced 1 1 100 41.170496 36.70864 4.461856 20.32290726300016 4674.9296875 2026-11-01T23:51:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k KR --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-balanced 29 Map report yeast Micro-C, every stored resolution mapreport chromosomix 0.19.0 at 997e59c 1 1 101 3.267181 3.021792 0.245389 2.7414234560001205 243.30078125 2026-11-01T23:51:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix mapreport data/GSE151553_A364_merged.mcool::/resolutions/800 --out mapreport/app 29 Map report yeast Micro-C, every stored resolution map-resolution cooler 0.10.4 1 1 102 5.675815 5.257541 0.418274 5.397954372998356 861.41015625 2026-11-01T23:51:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/map_resolution.py data/GSE151553_A364_merged.mcool mapreport/cooler.tsv 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb cooltools-insulation cooltools 0.7.1 4 2 1 11.704837 10.959245 0.7455919999999999 5.122559634999561 886.8447265625 2026-11-01T23:51:35 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 insulation/cooltools.tsv 4 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb insulation chromosomix 0.19.0 at 997e59c 1 2 0 4.865582 4.381561 0.484021 3.8950025600006484 300.88671875 2026-11-01T23:51:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --window 10 --out insulation/app 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb domaincaller-di domaincaller 0.1.0 1 2 3 2.71918 2.577121 0.142059 2.4369620340003166 258.56640625 2026-11-01T23:51:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/domaincaller_di.py data/4DNFIOZ1TRUS.mcool::/resolutions/50000 di/domaincaller.npy 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb di chromosomix 0.19.0 at 997e59c 1 2 2 2.338008 2.178667 0.15934099999999998 1.7521607350008708 215.390625 2026-11-01T23:51:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix di data/4DNFIOZ1TRUS.mcool::/resolutions/50000 --window 40 --out di/app 3 Compartments mouse Hi-C, 100 kb, GC-phased cooltools-eigs cooltools 0.7.1 1 2 5 15.231029 14.686231 0.544798 7.832449211000494 560.25 2026-11-01T23:51:48 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_eigs_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 compartments/gc.tsv compartments/cooltools 3 Compartments mouse Hi-C, 100 kb, GC-phased compartments chromosomix 0.19.0 at 997e59c 1 2 4 5.985633 5.649633 0.33599999999999997 4.366538596999817 300.54296875 2026-11-01T23:51:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix compartments data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --components 3 --phaseTrack compartments/gc.bedGraph --out compartments/app 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-yeast cooltools 0.7.1 yeast 800 bp yeast 800 bp 4 2 8 3.024447 2.533214 0.491233 2.375247998999839 957.78515625 2026-11-01T23:52:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/GSE151553_A364_merged.mcool::/resolutions/800 ps/yeast-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-mouse cooltools 0.7.1 mouse 10 kb mouse 10 kb 4 2 9 25.171300000000002 16.134512 9.036788 9.91419618799955 11705.630859375 2026-11-01T23:52:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 ps/mouse-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-yeast chromosomix 0.19.0 at 997e59c yeast 800 bp yeast 800 bp 1 2 6 0.6778409999999999 0.581722 0.096119 0.5256771580006898 211.578125 2026-11-01T23:52:13 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/GSE151553_A364_merged.mcool::/resolutions/800 --quantity expected --scope file --out ps/yeast 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-mouse chromosomix 0.19.0 at 997e59c mouse 10 kb mouse 10 kb 1 2 7 2.890617 2.562456 0.328161 2.382231777000925 237.9921875 2026-11-01T23:52:13 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --quantity expected --scope file --out ps/mouse 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 seed 0 seed 0 1 2 11 61.765515 58.166476 3.599039 61.903744365999955 1667.7890625 2026-11-01T23:52:16 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 yapc/seed0/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 peaks chromosomix 0.19.0 at 997e59c 1 2 10 20.00337 18.452155 1.551215 18.216484235999815 300.33203125 2026-11-01T23:53:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/4DNFIIY4QW2D.chr19.bw --replicate data/4DNFITBRHVZE.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out yapc/app 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosight 1.6.3 4 2 13 30.334837 28.973212 1.361625 10.647978555000009 770.8828125 2026-11-01T23:53:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight detect --pattern loops --threads 4 data/GSE151553_A364_merged.mcool::/resolutions/800 loops/chromosight/loops 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosomix 0.19.0 at 997e59c 1 2 12 6.1747119999999995 5.935452 0.23926 5.0408245459984755 268.92578125 2026-11-01T23:53:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix chromosight data/GSE151553_A364_merged.mcool::/resolutions/800 --pattern loops --out loops/app 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep hicrep 0.2.6 3 maps, 3 pairs 3 maps, 3 pairs 1 2 15 5.486293 5.211965 0.27432799999999996 5.230043874998955 257.9375 2026-11-01T23:53:52 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/hicrep_scc.py hicrep/hicrep.tsv chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ 4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000 4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000 4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep chromosomix 0.19.0 at 997e59c 3 maps, 3 pairs 3 maps, 3 pairs 1 2 14 3.930872 3.65763 0.273242 3.1568720390005183 254.734375 2026-11-01T23:53:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix hicrep data/4DNFIH8L6WON.mcool::/resolutions/100000 --against data/4DNFITBCUX56.mcool::/resolutions/100000 --against data/4DNFIIML46E5.mcool::/resolutions/100000 --maxDistance 50 --smooth 1 --no-balance --sequences chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ --out hicrep/app 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads pastis-seed0 pastis 0.5.0 seed 0 seed 0 1 2 17 82.335441 79.044774 3.290667 29.77211424899906 359.15234375 2026-11-01T23:54:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed0.npy 0 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads reconstruct3d-seed0 chromosomix 0.19.0 at 997e59c seed 0 seed 0 1 2 16 5.728899 5.589635 0.139264 5.4347186329996475 211.578125 2026-11-01T23:54:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 0 --out pastis/app-seed0 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-raw cooltools 0.7.1 raw raw 4 2 20 5.863528 5.02091 0.842618 2.6887326810010563 1184.5107421875 2026-11-01T23:54:35 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-raw.tsv 4 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-balanced cooltools 0.7.1 balanced balanced 4 2 21 6.087225999999999 5.378797 0.708429 2.9245690969983116 1825.6943359375 2026-11-01T23:54:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-balanced.tsv 4 weight 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-raw chromosomix 0.19.0 at 997e59c raw raw 1 2 18 3.7579960000000003 3.366372 0.39162399999999997 3.124125577000086 372.32421875 2026-11-01T23:54:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --out coverage/raw 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 2 19 4.012624 3.558893 0.453731 3.3275021389999893 270.73828125 2026-11-01T23:54:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --balance --out coverage/balanced 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome cooltools-virtual4c-Sox2 cooltools 0.7.1 Sox2 Sox2 4 2 23 7.154725999999999 6.565293 0.589433 2.9805251260004297 524.08203125 2026-11-01T23:54:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr3:34650000-34660000 virtual4c/cooltools-Sox2.tsv 4 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome fourc-Sox2 chromosomix 0.19.0 at 997e59c Sox2 Sox2 1 2 22 1.223092 1.043463 0.17962899999999998 0.921730779000427 276.21875 2026-11-01T23:54:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr3:34,650,001-34,660,000 --no-cis --out virtual4c/Sox2 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw coolpuppy 1.1.0 raw raw 4 2 28 8.52954 7.683566 0.845974 3.3985368269986793 955.9462890625 2026-11-01T23:54:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw-every coolpuppy 1.1.0 raw, every loop raw, every loop 4 2 29 8.759102 7.844114 0.9149879999999999 3.5044631119999394 886.861328125 2026-11-01T23:54:55 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw-every.tsv 4 --mindist 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-local coolpuppy 1.1.0 on the diagonal, raw on the diagonal, raw 4 2 30 9.236574000000001 8.327932 0.908642 3.614983854999082 846.8916015625 2026-11-01T23:54:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local.tsv 4 --local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-controls-seed0 coolpuppy 1.1.0 controls, seed 0 controls 4 2 31 9.005373 8.078562 0.9268109999999999 3.536624030000894 881.2890625 2026-11-01T23:55:02 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed0.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw chromosomix 0.19.0 at 997e59c raw raw 1 2 24 1.3754439999999999 1.236298 0.139146 0.9495775079994928 211.578125 2026-11-01T23:55:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/raw 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw-every chromosomix 0.19.0 at 997e59c raw, every loop raw, every loop 1 2 25 2.026531 1.838984 0.187547 1.4466721170010715 211.578125 2026-11-01T23:55:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/raw-every 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-local chromosomix 0.19.0 at 997e59c on the diagonal, raw on the diagonal, raw 1 2 26 2.25208 2.038173 0.21390699999999999 1.5642951089994312 211.578125 2026-11-01T23:55:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm none --mode fixed --window 5 --minDiag 2 --out apa/local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-controls-seed1 chromosomix 0.19.0 at 997e59c controls, seed 1 controls 1 2 27 2.4393130000000003 2.254227 0.185086 1.7447289939991606 211.578125 2026-11-01T23:55:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 1 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed1 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops chromosight-quantify chromosight 1.6.3 4 2 33 81.828225 78.406713 3.421512 25.93982210899958 1462.5244140625 2026-11-01T23:55:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight quantify --pattern loops --threads 4 apa/loops.bedpe data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chromosight-quantify/quantify 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops apa-chromosight chromosomix 0.19.0 at 997e59c 1 2 32 4.968702 4.75603 0.212672 3.6890037020002637 249.296875 2026-11-01T23:55:37 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm chromosight --out chromosight-quantify/app 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boosthic-chr1 Boost-HiC a615aff chr1, 1,955 bins chr1, 1,955 bins 1 2 35 19.947051000000002 19.737031 0.21001999999999998 19.44321442799992 462.4765625 2026-11-01T23:55:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr1 boost-hic/boosthic-chr1 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boost-chr1 chromosomix 0.19.0 at 997e59c chr1, 1,955 bins chr1, 1,955 bins 1 2 34 3.2923430000000002 2.879551 0.412792 3.0574121410008956 638.3046875 2026-11-01T23:56:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr1 --out boost-hic/chr1 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix deepTools 4.0.0 computeMatrix TSS 4 2 38 3.325414 2.939018 0.38639599999999996 3.281986390999009 211.578125 2026-11-01T23:56:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile deepTools 4.0.0 plotProfile TSS 1 2 39 1.8416979999999998 1.7217829999999998 0.119915 1.5390142420001212 222.4921875 2026-11-01T23:56:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools.mat.gz -out metaplot/deeptools-profile.png --outFileNameData metaplot/deeptools-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix-two deepTools 4.0.0 computeMatrix TSS, two tracks 4 2 40 6.219252 5.57108 0.648172 3.8800419099989085 245.0859375 2026-11-01T23:56:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw data/4DNFITBRHVZE.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools-two.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile-two deepTools 4.0.0 plotProfile TSS, two tracks 1 2 41 2.5308640000000002 2.411918 0.118946 2.2280643499998405 262.76953125 2026-11-01T23:56:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-profile.png --outFileNameData metaplot/deeptools-two-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotheatmap-two deepTools 4.0.0 plotHeatmap TSS, two tracks 1 2 42 3.243629 2.9956579999999997 0.247971 2.9479712510001264 484.625 2026-11-01T23:56:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-heatmap.png --outFileSortedRegions metaplot/deeptools-two-heatmap.bed 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot chromosomix 0.19.0 at 997e59c TSS 1 2 36 4.196898 3.525272 0.671626 3.3754425419992913 383.1015625 2026-11-01T23:56:17 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot-two chromosomix 0.19.0 at 997e59c TSS, two tracks 1 2 37 7.619320999999999 6.397384 1.221937 6.244317605998731 439.16015625 2026-11-01T23:56:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --tracks data/4DNFITBRHVZE.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app-two 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 bedtools-overlap bedtools 2.31.1 1 2 44 40.666714999999996 27.497964 13.168751 36.436976822998986 211.578125 2026-11-01T23:56:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bedtools_overlap.py yapc/seed0/yapc_0.05.bed overlap/promoters.bed overlap/mm10.genome 1000 overlap/bedtools 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 overlap chromosomix 0.19.0 at 997e59c 1 2 43 1.063117 1.037041 0.026076 0.9887909899989609 211.578125 2026-11-01T23:57:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix overlap --sequence data/mm10.fa --features yapc/seed0/yapc_0.05.bed --features overlap/promoters.bed --a yapc/seed0/yapc_0.05.bed --b overlap/promoters.bed --shuffle --iterations 1000 --seed 1 --out overlap/app 16 Base composition mm10, 10 kb bins composition bioframe, Biopython 0.8.0, 1.88 1 2 46 39.643135 33.169113 6.474022 43.04428058200028 507.73046875 2026-11-01T23:57:04 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/composition.py data/mm10.fa 10000 composition/reference.tsv 16 Base composition mm10, 10 kb bins composition chromosomix 0.19.0 at 997e59c 1 2 45 3.593209 3.065978 0.527231 2.9518309459999728 294.40234375 2026-11-01T23:57:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix composition --sequence data/mm10.fa --resolution 10000 --out composition/app 17 Motif search mm10 chr19, two motifs, both strands seqkit-TGACTCA seqkit 2.3.0 TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 4 2 49 18.47726 16.835151 1.642109 18.32143828900007 4118.4296875 2026-11-01T23:57:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -m 1 -p TGACTCA --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-TGACTCA.bed 17 Motif search mm10 chr19, two motifs, both strands seqkit-WGATAR seqkit 2.3.0 WGATAR WGATAR 4 2 50 6.382516 6.191516 0.191 6.103582858000664 343.63671875 2026-11-01T23:58:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -d -p WGATAR --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-WGATAR.bed 17 Motif search mm10 chr19, two motifs, both strands motif-TGACTCA chromosomix 0.19.0 at 997e59c TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 1 2 47 5.23371 2.719872 2.513838 5.2015628820008715 359.7734375 2026-11-01T23:58:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern TGACTCA --mismatches 1 --out motif/TGACTCA 17 Motif search mm10 chr19, two motifs, both strands motif-WGATAR chromosomix 0.19.0 at 997e59c WGATAR WGATAR 1 2 48 3.959295 2.08898 1.870315 3.968219176000275 323.734375 2026-11-01T23:58:20 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern WGATAR --mismatches 0 --out motif/WGATAR 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-100 deepTools 4.0.0 100 bp, the windows 100 bp windows 4 2 57 188.800945 184.123513 4.677432 49.82843171899913 304.6640625 2026-11-01T23:58:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 100 -p 4 -o trackcorr/deeptools-100.npz --outRawCounts trackcorr/deeptools-100.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-pearson deepTools 4.0.0 100 bp, pearson 100 bp windows 1 2 58 1.672446 1.5313240000000001 0.141122 1.0592549700013478 270.734375 2026-11-01T23:59:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c pearson -p heatmap -o trackcorr/deeptools-100-pearson.png --outFileCorMatrix trackcorr/deeptools-100-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-spearman deepTools 4.0.0 100 bp, spearman 100 bp windows 1 2 59 2.031013 1.868853 0.16216 1.4139903929990396 270.78515625 2026-11-01T23:59:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c spearman -p heatmap -o trackcorr/deeptools-100-spearman.png --outFileCorMatrix trackcorr/deeptools-100-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-1000 deepTools 4.0.0 1,000 bp, the windows 1,000 bp windows 4 2 60 17.661348 17.165305 0.49604299999999996 4.800462127999708 211.578125 2026-11-01T23:59:16 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 1000 -p 4 -o trackcorr/deeptools-1000.npz --outRawCounts trackcorr/deeptools-1000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-pearson deepTools 4.0.0 1,000 bp, pearson 1,000 bp windows 1 2 61 1.387635 1.283588 0.104047 0.7700924629989458 211.578125 2026-11-01T23:59:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c pearson -p heatmap -o trackcorr/deeptools-1000-pearson.png --outFileCorMatrix trackcorr/deeptools-1000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-spearman deepTools 4.0.0 1,000 bp, spearman 1,000 bp windows 1 2 62 1.41204 1.312108 0.09993199999999999 0.7941332709997369 211.578125 2026-11-01T23:59:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c spearman -p heatmap -o trackcorr/deeptools-1000-spearman.png --outFileCorMatrix trackcorr/deeptools-1000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-10000 deepTools 4.0.0 10,000 bp, the windows 10,000 bp windows 4 2 63 2.308299 2.187483 0.12081599999999999 0.6980180230002588 211.578125 2026-11-01T23:59:23 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 10000 -p 4 -o trackcorr/deeptools-10000.npz --outRawCounts trackcorr/deeptools-10000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-pearson deepTools 4.0.0 10,000 bp, pearson 10,000 bp windows 1 2 64 1.3523349999999998 1.2684389999999999 0.083896 0.734184083999935 211.578125 2026-11-01T23:59:23 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c pearson -p heatmap -o trackcorr/deeptools-10000-pearson.png --outFileCorMatrix trackcorr/deeptools-10000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-spearman deepTools 4.0.0 10,000 bp, spearman 10,000 bp windows 1 2 65 1.349142 1.268373 0.080769 0.7415905990001193 211.578125 2026-11-01T23:59:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c spearman -p heatmap -o trackcorr/deeptools-10000-spearman.png --outFileCorMatrix trackcorr/deeptools-10000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-pearson chromosomix 0.19.0 at 997e59c 100 bp, pearson 100 bp windows 1 2 51 0.73942 0.649763 0.089657 0.5497804360002192 211.578125 2026-11-01T23:59:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method pearson --out trackcorr/app-100-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-spearman chromosomix 0.19.0 at 997e59c 100 bp, spearman 100 bp windows 1 2 52 1.586624 1.412556 0.174068 1.34433166800045 316.375 2026-11-01T23:59:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method spearman --out trackcorr/app-100-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-pearson chromosomix 0.19.0 at 997e59c 1,000 bp, pearson 1,000 bp windows 1 2 53 0.695564 0.635774 0.059789999999999996 0.4841159389998211 211.578125 2026-11-01T23:59:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method pearson --out trackcorr/app-1000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-spearman chromosomix 0.19.0 at 997e59c 1,000 bp, spearman 1,000 bp windows 1 2 54 0.8106079999999999 0.7230019999999999 0.08760599999999999 0.5691757130007318 211.578125 2026-11-01T23:59:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method spearman --out trackcorr/app-1000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-pearson chromosomix 0.19.0 at 997e59c 10,000 bp, pearson 10,000 bp windows 1 2 55 0.7065 0.626881 0.079619 0.49281068600066646 211.578125 2026-11-01T23:59:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method pearson --out trackcorr/app-10000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-spearman chromosomix 0.19.0 at 997e59c 10,000 bp, spearman 10,000 bp windows 1 2 56 0.752324 0.6800619999999999 0.07226199999999999 0.5008532650008419 211.578125 2026-11-01T23:59:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method spearman --out trackcorr/app-10000-spearman 19 Loop calling mouse Hi-C, 10 kb, every chromosome cooltools-dots cooltools 0.7.1 4 2 67 549.727708 504.748878 44.97883 154.06106792500032 9692.9404296875 2026-11-01T23:59:29 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_dots.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 loopcalling/cooltools.tsv 4 19 Loop calling mouse Hi-C, 10 kb, every chromosome loops chromosomix 0.19.0 at 997e59c 1 2 66 24.974377 23.400573 1.573804 21.689090191001014 451.51953125 2026-11-02T00:02:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix loops data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --out loopcalling/app 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches pybigwig-groupsignal-entries pyBigWig, SciPy 0.3.26, 1.16.3 one value per entry one value per entry 1 2 69 1.43689 1.31639 0.1205 0.8804132120003487 211.578125 2026-11-02T00:02:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 0 groupsignal/reference-entries data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches groupsignal-entries chromosomix 0.19.0 at 997e59c one value per entry one value per entry 1 2 68 0.655289 0.567589 0.0877 0.4707480819997727 211.578125 2026-11-02T00:02:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --out groupsignal/app-entries 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-cooltools-insulation cooltools 0.7.1 insulation, four scales insulation 4 2 76 5.686955 5.206666 0.48028899999999997 5.087176407998413 807.0166015625 2026-11-02T00:02:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation_scales.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/insulation/cooltools.tsv 4 50000 100000 200000 400000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 peaks, seed 0 peaks 1 2 77 79.10215299999999 75.989967 3.112186 79.22010048799893 1595.71484375 2026-11-02T00:02:31 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 gm12878/yapc/seed0/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw coolpuppy 1.1.0 APA, raw APA 4 2 78 3.385913 2.876248 0.5096649999999999 2.900346542999614 1088.71875 2026-11-02T00:03:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw.tsv 4 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw-every coolpuppy 1.1.0 APA, raw, every pair APA 4 2 79 3.570662 3.062812 0.50785 3.083235528998557 1123.3974609375 2026-11-02T00:03:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw-every.tsv 4 --mindist 0 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-signal deepTools 4.0.0 computeMatrix metaplot, signal 4 2 80 0.797639 0.7404499999999999 0.057189 0.3967718479998439 211.578125 2026-11-02T00:03:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw data/ENCFF487LOB.chr19.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 2000 -a 2000 --binSize 50 -p 4 -o gm12878/metaplot/deeptools-signal.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-signal deepTools 4.0.0 plotProfile metaplot, signal 1 2 81 1.015561 0.9586979999999999 0.056863 0.7119341890011128 211.578125 2026-11-02T00:03:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-profile.png --outFileNameData gm12878/metaplot/deeptools-signal-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-signal deepTools 4.0.0 plotHeatmap metaplot, signal 1 2 82 1.4065269999999999 1.30649 0.100037 1.0990404510012013 211.578125 2026-11-02T00:03:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-signal-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-insulation deepTools 4.0.0 computeMatrix metaplot, insulation 4 2 83 38.002494 28.919370999999998 9.083123 10.892291420999754 945.83984375 2026-11-02T00:03:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 500000 -a 500000 --binSize 10000 -p 4 -o gm12878/metaplot/deeptools-insulation.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-insulation deepTools 4.0.0 plotProfile metaplot, insulation 1 2 84 1.157176 1.086288 0.07088799999999999 0.8499001139989559 211.578125 2026-11-02T00:04:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-profile.png --outFileNameData gm12878/metaplot/deeptools-insulation-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-insulation deepTools 4.0.0 plotHeatmap metaplot, insulation 1 2 85 1.668998 1.582155 0.08684299999999999 1.381841581000117 211.578125 2026-11-02T00:04:10 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-insulation-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-insulation chromosomix 0.19.0 at 997e59c insulation, four scales insulation 1 2 70 1.341622 1.202868 0.138754 0.9887220279997564 211.578125 2026-11-02T00:04:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIXP4QG5B_10000.chr19.cool --window 5 --scales 4 --out gm12878/insulation/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-peaks chromosomix 0.19.0 at 997e59c peaks peaks 1 2 71 40.133120999999996 38.609041 1.52408 37.616281749000336 221.859375 2026-11-02T00:04:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/ENCFF734CUT.chr19.bw --replicate data/ENCFF644EEX.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out gm12878/yapc/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw chromosomix 0.19.0 at 997e59c APA, raw APA 1 2 72 0.744523 0.636463 0.10805999999999999 0.5152811619991553 211.578125 2026-11-02T00:04:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw-every chromosomix 0.19.0 at 997e59c APA, raw, every pair APA 1 2 73 1.1613159999999998 1.004055 0.15726099999999998 0.8374726760011981 224.87109375 2026-11-02T00:04:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw-every 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-signal chromosomix 0.19.0 at 997e59c metaplot, CTCF and ATAC-seq, ±2 kb metaplot, signal 1 2 74 1.182786 0.983784 0.19900199999999998 0.8755690429989045 272.6171875 2026-11-02T00:04:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/ENCFF734CUT.chr19.bw --tracks data/ENCFF644EEX.chr19.bw --tracks data/ENCFF487LOB.chr19.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 2000 --step 50 --band none --out gm12878/metaplot/app-signal 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-insulation chromosomix 0.19.0 at 997e59c metaplot, insulation at four scales, ±500 kb metaplot, insulation 1 2 75 1.242615 1.030116 0.212499 0.9914512319992355 211.578125 2026-11-02T00:04:52 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 500000 --step 10000 --band none --out gm12878/metaplot/app-insulation 25 Pairs statistics yeast Hi-C contact list, deduplicated pairtools-stats pairtools 1.1.2 1 2 87 87.17632699999999 77.765577 9.41075 77.94446497100034 306.9453125 2026-11-02T00:04:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 25 Pairs statistics yeast Hi-C contact list, deduplicated pairstats chromosomix 0.19.0 at 997e59c 1 2 86 69.878137 48.071262 21.806875 62.23644568999953 295.0078125 2026-11-02T00:06:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix stats data/CH128.pairs.gz --out pairstats/app 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins bioframe-digest bioframe, Biopython 0.8.0, 1.88 1 2 89 1.218062 1.128132 0.08993 0.9198783280007774 211.578125 2026-11-02T00:07:13 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bioframe_digest.py data/R64-1-1.fa DpnII 5000 restriction/digest -2 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins restriction chromosomix 0.19.0 at 997e59c 1 2 88 1.205133 0.6320549999999999 0.573078 1.1145754619992658 211.578125 2026-11-02T00:07:14 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix restriction restriction/CH128.5000.cool --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-sites 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooler-cload cooler 0.10.4 1 2 91 44.37892 43.230134 1.148786 44.147564883000086 2399.140625 2026-11-02T00:07:16 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 data/R64-1-1.chrom.sizes:5000 data/CH128.pairs.gz restriction/CH128.5000.cool 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-top pairtools 1.1.2 1 2 92 339.51328 329.163174 10.350106 203.81316039599915 211.578125 2026-11-02T00:08:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags.bed data/CH128.pairs.gz -o restriction/CH128.restricted.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-bottom pairtools 1.1.2 1 2 93 338.22024999999996 328.250322 9.969928 203.37128562600083 211.578125 2026-11-02T00:11:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags-bottom.bed data/CH128.pairs.gz -o restriction/CH128.restricted-bottom.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb restriction-reference pandas 2.3.3 1 2 94 78.158553 75.97851 2.180043 78.97832937599924 854.12890625 2026-11-02T00:14:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/restriction_reference.py data/R64-1-1.fa DpnII restriction/CH128.restricted.pairs.gz restriction/CH128.restricted-bottom.pairs.gz restriction/pairtools -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooltools-coverage-sites cooltools 0.7.1 4 2 95 2.367607 2.073209 0.294398 1.7160723139986658 296.4765625 2026-11-02T00:16:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage_sites.py restriction/CH128.5000.cool restriction/digest.sites.tsv restriction/coverage 4 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc-pairtools-stats pairtools 1.1.2 1 2 96 86.687048 77.040368 9.64668 76.97762606599827 308.5546875 2026-11-02T00:16:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc chromosomix 0.19.0 at 997e59c 1 2 90 136.886952 94.969093 41.917859 121.68073907800135 331.11328125 2026-11-02T00:17:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix pairsqc data/CH128.pairs.gz --bin-size 5000 --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-pairsqc 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-raw Juicer Tools 1.22.01, on Java 21.0.13 raw raw 1 2 99 41.653999 37.334808 4.319191 21.247383803000048 2649.16796875 2026-11-02T00:19:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k NONE --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-balanced Juicer Tools 1.22.01, on Java 21.0.13 balanced balanced 1 2 100 41.826689 37.312117 4.514572 21.17939214600119 3742.40625 2026-11-02T00:19:48 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k KR --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-balanced 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-raw chromosomix 0.19.0 at 997e59c raw raw 1 2 97 5.818754 5.126832 0.6919219999999999 5.951939898001001 511.8359375 2026-11-02T00:20:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --no-balance --out arrowhead/app-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 2 98 6.062891 5.247755 0.815136 6.369169485999009 553.11328125 2026-11-02T00:20:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --out arrowhead/app-balanced 29 Map report yeast Micro-C, every stored resolution map-resolution cooler 0.10.4 1 2 102 5.6872750000000005 5.253426 0.433849 5.447519366000051 861.26171875 2026-11-02T00:20:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/map_resolution.py data/GSE151553_A364_merged.mcool mapreport/cooler.tsv 29 Map report yeast Micro-C, every stored resolution mapreport chromosomix 0.19.0 at 997e59c 1 2 101 3.2520179999999996 2.9712899999999998 0.280728 2.720095703998595 234.94140625 2026-11-02T00:20:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix mapreport data/GSE151553_A364_merged.mcool::/resolutions/800 --out mapreport/app 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb insulation chromosomix 0.19.0 at 997e59c 1 3 0 4.989057 4.469025 0.5200319999999999 3.9025276510001277 294.59765625 2026-11-02T00:20:29 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --window 10 --out insulation/app 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb cooltools-insulation cooltools 0.7.1 4 3 1 11.672282 10.867825 0.804457 5.048287472000084 888.3564453125 2026-11-02T00:20:33 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 insulation/cooltools.tsv 4 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb di chromosomix 0.19.0 at 997e59c 1 3 2 2.383877 2.217796 0.16608099999999998 1.8427779820012802 211.578125 2026-11-02T00:20:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix di data/4DNFIOZ1TRUS.mcool::/resolutions/50000 --window 40 --out di/app 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb domaincaller-di domaincaller 0.1.0 1 3 3 2.764811 2.595825 0.168986 2.459959007001089 258.4375 2026-11-02T00:20:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/domaincaller_di.py data/4DNFIOZ1TRUS.mcool::/resolutions/50000 di/domaincaller.npy 3 Compartments mouse Hi-C, 100 kb, GC-phased compartments chromosomix 0.19.0 at 997e59c 1 3 4 6.228622 5.880974 0.34764799999999996 4.480085536000843 297.234375 2026-11-02T00:20:43 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix compartments data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --components 3 --phaseTrack compartments/gc.bedGraph --out compartments/app 3 Compartments mouse Hi-C, 100 kb, GC-phased cooltools-eigs cooltools 0.7.1 1 3 5 14.656232000000001 14.112016 0.5442159999999999 7.493206163999275 560.3125 2026-11-02T00:20:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_eigs_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 compartments/gc.tsv compartments/cooltools 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-yeast chromosomix 0.19.0 at 997e59c yeast 800 bp yeast 800 bp 1 3 6 0.6841119999999999 0.5841189999999999 0.099993 0.5174840740000946 211.578125 2026-11-02T00:20:55 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/GSE151553_A364_merged.mcool::/resolutions/800 --quantity expected --scope file --out ps/yeast 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-mouse chromosomix 0.19.0 at 997e59c mouse 10 kb mouse 10 kb 1 3 7 2.88704 2.598737 0.288303 2.375473864000014 237.15625 2026-11-02T00:20:55 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --quantity expected --scope file --out ps/mouse 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-yeast cooltools 0.7.1 yeast 800 bp yeast 800 bp 4 3 8 3.016492 2.54642 0.470072 2.3641968479987554 956.94921875 2026-11-02T00:20:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/GSE151553_A364_merged.mcool::/resolutions/800 ps/yeast-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-mouse cooltools 0.7.1 mouse 10 kb mouse 10 kb 4 3 9 25.857421000000002 16.446909 9.410512 9.254308052999477 11449.669921875 2026-11-02T00:21:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 ps/mouse-cooltools.tsv 4 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 peaks chromosomix 0.19.0 at 997e59c 1 3 10 20.467121000000002 18.735468 1.731653 18.71835091400135 269.35546875 2026-11-02T00:21:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/4DNFIIY4QW2D.chr19.bw --replicate data/4DNFITBRHVZE.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out yapc/app 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 seed 0 seed 0 1 3 11 62.269497 58.948938 3.320559 62.408848109000246 1667.546875 2026-11-02T00:21:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 yapc/seed0/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosomix 0.19.0 at 997e59c 1 3 12 6.463705 6.212746 0.250959 5.306311872000151 270.31640625 2026-11-02T00:22:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix chromosight data/GSE151553_A364_merged.mcool::/resolutions/800 --pattern loops --out loops/app 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosight 1.6.3 4 3 13 31.955727 30.550346 1.405381 11.306467777998478 714.69921875 2026-11-02T00:22:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight detect --pattern loops --threads 4 data/GSE151553_A364_merged.mcool::/resolutions/800 loops/chromosight/loops 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep chromosomix 0.19.0 at 997e59c 3 maps, 3 pairs 3 maps, 3 pairs 1 3 14 4.28421 4.007616 0.276594 3.4140613349991327 256.34375 2026-11-02T00:22:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix hicrep data/4DNFIH8L6WON.mcool::/resolutions/100000 --against data/4DNFITBCUX56.mcool::/resolutions/100000 --against data/4DNFIIML46E5.mcool::/resolutions/100000 --maxDistance 50 --smooth 1 --no-balance --sequences chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ --out hicrep/app 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep hicrep 0.2.6 3 maps, 3 pairs 3 maps, 3 pairs 1 3 15 5.767462 5.518185 0.249277 5.468591720000404 260.94140625 2026-11-02T00:22:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/hicrep_scc.py hicrep/hicrep.tsv chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ 4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000 4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000 4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads reconstruct3d-seed0 chromosomix 0.19.0 at 997e59c seed 0 seed 0 1 3 16 5.9036859999999995 5.717254 0.186432 5.598124101001304 211.578125 2026-11-02T00:22:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 0 --out pastis/app-seed0 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads pastis-seed0 pastis 0.5.0 seed 0 seed 0 1 3 17 84.717915 81.281242 3.436673 31.420947893999255 358.93359375 2026-11-02T00:23:02 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed0.npy 0 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-raw chromosomix 0.19.0 at 997e59c raw raw 1 3 18 4.065476 3.634108 0.431368 3.3128365419997863 372.9140625 2026-11-02T00:23:33 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --out coverage/raw 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 3 19 4.299097 3.8361799999999997 0.46291699999999997 3.5857370579997223 273.24609375 2026-11-02T00:23:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --balance --out coverage/balanced 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-raw cooltools 0.7.1 raw raw 4 3 20 6.058133000000001 5.3241060000000004 0.734027 2.873530765000396 1065.5078125 2026-11-02T00:23:40 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-raw.tsv 4 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-balanced cooltools 0.7.1 balanced balanced 4 3 21 6.511793 5.748089 0.7637039999999999 3.2010094199995365 1306.87890625 2026-11-02T00:23:43 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-balanced.tsv 4 weight 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome fourc-Sox2 chromosomix 0.19.0 at 997e59c Sox2 Sox2 1 3 22 1.288211 1.124294 0.16391699999999998 0.980332957000428 263.9296875 2026-11-02T00:23:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr3:34,650,001-34,660,000 --no-cis --out virtual4c/Sox2 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome cooltools-virtual4c-Sox2 cooltools 0.7.1 Sox2 Sox2 4 3 23 7.208141 6.684451 0.52369 3.0636708550009644 555.2236328125 2026-11-02T00:23:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr3:34650000-34660000 virtual4c/cooltools-Sox2.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw chromosomix 0.19.0 at 997e59c raw raw 1 3 24 1.3440569999999998 1.211741 0.132316 0.9226506420000078 211.578125 2026-11-02T00:23:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/raw 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw-every chromosomix 0.19.0 at 997e59c raw, every loop raw, every loop 1 3 25 2.077787 1.922129 0.155658 1.480186507000326 211.578125 2026-11-02T00:23:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/raw-every 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-local chromosomix 0.19.0 at 997e59c on the diagonal, raw on the diagonal, raw 1 3 26 2.2717259999999997 2.075106 0.19662 1.5823243750000984 218.29296875 2026-11-02T00:23:52 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm none --mode fixed --window 5 --minDiag 2 --out apa/local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-controls-seed1 chromosomix 0.19.0 at 997e59c controls, seed 1 controls 1 3 27 2.487494 2.327591 0.159903 1.7394693729984283 211.578125 2026-11-02T00:23:54 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 1 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed1 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw coolpuppy 1.1.0 raw raw 4 3 28 9.092695 8.225213 0.867482 3.7837379120010155 893.505859375 2026-11-02T00:23:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw-every coolpuppy 1.1.0 raw, every loop raw, every loop 4 3 29 9.588915 8.604901 0.9840139999999999 3.9088645909996558 882.1572265625 2026-11-02T00:23:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw-every.tsv 4 --mindist 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-local coolpuppy 1.1.0 on the diagonal, raw on the diagonal, raw 4 3 30 9.971413 9.018503 0.9529099999999999 3.941430274000595 993.6796875 2026-11-02T00:24:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local.tsv 4 --local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-controls-seed0 coolpuppy 1.1.0 controls, seed 0 controls 4 3 31 9.340045 8.426046 0.913999 3.6943873679992976 1015.373046875 2026-11-02T00:24:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed0.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 0 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops apa-chromosight chromosomix 0.19.0 at 997e59c 1 3 32 5.199237 4.963458 0.235779 3.8126187779998872 245.65625 2026-11-02T00:24:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm chromosight --out chromosight-quantify/app 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops chromosight-quantify chromosight 1.6.3 4 3 33 85.814099 82.272138 3.541961 27.353692654000042 1467.416015625 2026-11-02T00:24:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight quantify --pattern loops --threads 4 apa/loops.bedpe data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chromosight-quantify/quantify 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boost-chr1 chromosomix 0.19.0 at 997e59c chr1, 1,955 bins chr1, 1,955 bins 1 3 34 3.777904 3.360357 0.417547 3.546494726000674 635.90234375 2026-11-02T00:24:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr1 --out boost-hic/chr1 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boosthic-chr1 Boost-HiC a615aff chr1, 1,955 bins chr1, 1,955 bins 1 3 35 20.651765 20.461575 0.19019 20.138414638999166 462.42578125 2026-11-02T00:24:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr1 boost-hic/boosthic-chr1 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot chromosomix 0.19.0 at 997e59c TSS 1 3 36 4.295906 3.629247 0.666659 3.4440953049997916 384.08984375 2026-11-02T00:25:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot-two chromosomix 0.19.0 at 997e59c TSS, two tracks 1 3 37 7.9030190000000005 6.673797 1.229222 6.368799468000361 436.62890625 2026-11-02T00:25:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --tracks data/4DNFITBRHVZE.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app-two 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix deepTools 4.0.0 computeMatrix TSS 4 3 38 3.4205 3.03778 0.38272 3.2977506360002735 211.578125 2026-11-02T00:25:16 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile deepTools 4.0.0 plotProfile TSS 1 3 39 1.923689 1.8057699999999999 0.117919 1.6189358060000814 219.9921875 2026-11-02T00:25:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools.mat.gz -out metaplot/deeptools-profile.png --outFileNameData metaplot/deeptools-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix-two deepTools 4.0.0 computeMatrix TSS, two tracks 4 3 40 6.242537 5.644061 0.598476 3.8661844369999017 244.9140625 2026-11-02T00:25:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw data/4DNFITBRHVZE.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools-two.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile-two deepTools 4.0.0 plotProfile TSS, two tracks 1 3 41 2.548722 2.426927 0.121795 2.2435349150000548 262.75 2026-11-02T00:25:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-profile.png --outFileNameData metaplot/deeptools-two-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotheatmap-two deepTools 4.0.0 plotHeatmap TSS, two tracks 1 3 42 3.226852 3.011796 0.215056 2.9252987999989273 487.7578125 2026-11-02T00:25:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-heatmap.png --outFileSortedRegions metaplot/deeptools-two-heatmap.bed 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 overlap chromosomix 0.19.0 at 997e59c 1 3 43 1.0401369999999999 1.002918 0.037218999999999995 0.9677866500005621 211.578125 2026-11-02T00:25:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix overlap --sequence data/mm10.fa --features yapc/seed0/yapc_0.05.bed --features overlap/promoters.bed --a yapc/seed0/yapc_0.05.bed --b overlap/promoters.bed --shuffle --iterations 1000 --seed 1 --out overlap/app 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 bedtools-overlap bedtools 2.31.1 1 3 44 43.957673 29.800177 14.157496 39.49515312400035 211.578125 2026-11-02T00:25:31 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bedtools_overlap.py yapc/seed0/yapc_0.05.bed overlap/promoters.bed overlap/mm10.genome 1000 overlap/bedtools 16 Base composition mm10, 10 kb bins composition chromosomix 0.19.0 at 997e59c 1 3 45 3.745713 3.048978 0.696735 7.6149995919986395 243.34375 2026-11-02T00:26:10 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix composition --sequence data/mm10.fa --resolution 10000 --out composition/app 16 Base composition mm10, 10 kb bins composition bioframe, Biopython 0.8.0, 1.88 1 3 46 40.041522 33.662917 6.378605 39.76383682999949 507.921875 2026-11-02T00:26:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/composition.py data/mm10.fa 10000 composition/reference.tsv 17 Motif search mm10 chr19, two motifs, both strands motif-TGACTCA chromosomix 0.19.0 at 997e59c TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 1 3 47 5.403274 2.654318 2.7489559999999997 5.427673648000564 359.75390625 2026-11-02T00:26:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern TGACTCA --mismatches 1 --out motif/TGACTCA 17 Motif search mm10 chr19, two motifs, both strands motif-WGATAR chromosomix 0.19.0 at 997e59c WGATAR WGATAR 1 3 48 4.392669 2.31048 2.082189 4.194191180000416 323.16796875 2026-11-02T00:27:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern WGATAR --mismatches 0 --out motif/WGATAR 17 Motif search mm10 chr19, two motifs, both strands seqkit-TGACTCA seqkit 2.3.0 TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 4 3 49 19.258490000000002 17.701056 1.557434 19.01947744899917 3942.7265625 2026-11-02T00:27:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -m 1 -p TGACTCA --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-TGACTCA.bed 17 Motif search mm10 chr19, two motifs, both strands seqkit-WGATAR seqkit 2.3.0 WGATAR WGATAR 4 3 50 6.300542999999999 6.111742 0.188801 6.011548791999303 343.15625 2026-11-02T00:27:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -d -p WGATAR --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-WGATAR.bed 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-pearson chromosomix 0.19.0 at 997e59c 100 bp, pearson 100 bp windows 1 3 51 0.7632099999999999 0.67348 0.08972999999999999 0.5797708919999423 211.578125 2026-11-02T00:27:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method pearson --out trackcorr/app-100-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-spearman chromosomix 0.19.0 at 997e59c 100 bp, spearman 100 bp windows 1 3 52 1.627098 1.449323 0.177775 1.3773566069994558 327.578125 2026-11-02T00:27:33 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method spearman --out trackcorr/app-100-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-pearson chromosomix 0.19.0 at 997e59c 1,000 bp, pearson 1,000 bp windows 1 3 53 0.738205 0.656625 0.08158 0.5090919319991372 211.578125 2026-11-02T00:27:34 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method pearson --out trackcorr/app-1000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-spearman chromosomix 0.19.0 at 997e59c 1,000 bp, spearman 1,000 bp windows 1 3 54 0.881871 0.792275 0.089596 0.6128371479990165 211.578125 2026-11-02T00:27:35 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method spearman --out trackcorr/app-1000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-pearson chromosomix 0.19.0 at 997e59c 10,000 bp, pearson 10,000 bp windows 1 3 55 0.742452 0.673798 0.06865399999999999 0.5033690460004436 211.578125 2026-11-02T00:27:35 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method pearson --out trackcorr/app-10000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-spearman chromosomix 0.19.0 at 997e59c 10,000 bp, spearman 10,000 bp windows 1 3 56 0.752535 0.686925 0.06561 0.5141630099988106 211.578125 2026-11-02T00:27:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method spearman --out trackcorr/app-10000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-100 deepTools 4.0.0 100 bp, the windows 100 bp windows 4 3 57 191.215722 186.370046 4.845676 50.443860490999214 306.779296875 2026-11-02T00:27:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 100 -p 4 -o trackcorr/deeptools-100.npz --outRawCounts trackcorr/deeptools-100.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-pearson deepTools 4.0.0 100 bp, pearson 100 bp windows 1 3 58 1.7841969999999998 1.6297 0.154497 1.1718640710005275 270.3671875 2026-11-02T00:28:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c pearson -p heatmap -o trackcorr/deeptools-100-pearson.png --outFileCorMatrix trackcorr/deeptools-100-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-spearman deepTools 4.0.0 100 bp, spearman 100 bp windows 1 3 59 2.1203089999999998 1.9669249999999998 0.153384 1.5067442919989844 270.04296875 2026-11-02T00:28:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c spearman -p heatmap -o trackcorr/deeptools-100-spearman.png --outFileCorMatrix trackcorr/deeptools-100-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-1000 deepTools 4.0.0 1,000 bp, the windows 1,000 bp windows 4 3 60 18.050148 17.556462 0.49368599999999996 4.8166870519999065 211.578125 2026-11-02T00:28:29 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 1000 -p 4 -o trackcorr/deeptools-1000.npz --outRawCounts trackcorr/deeptools-1000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-pearson deepTools 4.0.0 1,000 bp, pearson 1,000 bp windows 1 3 61 1.4656550000000002 1.369809 0.095846 0.8473667670004943 211.578125 2026-11-02T00:28:34 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c pearson -p heatmap -o trackcorr/deeptools-1000-pearson.png --outFileCorMatrix trackcorr/deeptools-1000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-spearman deepTools 4.0.0 1,000 bp, spearman 1,000 bp windows 1 3 62 1.555351 1.451261 0.10409 0.9369077000010293 211.578125 2026-11-02T00:28:35 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c spearman -p heatmap -o trackcorr/deeptools-1000-spearman.png --outFileCorMatrix trackcorr/deeptools-1000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-10000 deepTools 4.0.0 10,000 bp, the windows 10,000 bp windows 4 3 63 2.3393960000000003 2.22237 0.11702599999999999 0.7218776009995054 211.578125 2026-11-02T00:28:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 10000 -p 4 -o trackcorr/deeptools-10000.npz --outRawCounts trackcorr/deeptools-10000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-pearson deepTools 4.0.0 10,000 bp, pearson 10,000 bp windows 1 3 64 1.502294 1.390496 0.111798 0.8895433750003576 211.578125 2026-11-02T00:28:37 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c pearson -p heatmap -o trackcorr/deeptools-10000-pearson.png --outFileCorMatrix trackcorr/deeptools-10000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-spearman deepTools 4.0.0 10,000 bp, spearman 10,000 bp windows 1 3 65 1.431887 1.338765 0.093122 0.8131629159997829 211.578125 2026-11-02T00:28:38 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c spearman -p heatmap -o trackcorr/deeptools-10000-spearman.png --outFileCorMatrix trackcorr/deeptools-10000-spearman.tab 19 Loop calling mouse Hi-C, 10 kb, every chromosome loops chromosomix 0.19.0 at 997e59c 1 3 66 26.382287 25.003854 1.378433 22.56529181299993 448.55078125 2026-11-02T00:28:39 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix loops data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --out loopcalling/app 19 Loop calling mouse Hi-C, 10 kb, every chromosome cooltools-dots cooltools 0.7.1 4 3 67 571.172574 525.328066 45.844508 160.05059614499987 11032.83203125 2026-11-02T00:29:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_dots.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 loopcalling/cooltools.tsv 4 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches groupsignal-entries chromosomix 0.19.0 at 997e59c one value per entry one value per entry 1 3 68 0.623773 0.536385 0.087388 0.4601442399998632 211.578125 2026-11-02T00:31:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --out groupsignal/app-entries 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches pybigwig-groupsignal-entries pyBigWig, SciPy 0.3.26, 1.16.3 one value per entry one value per entry 1 3 69 1.428402 1.319828 0.10857399999999999 0.8572707759994955 211.578125 2026-11-02T00:31:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 0 groupsignal/reference-entries data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-insulation chromosomix 0.19.0 at 997e59c insulation, four scales insulation 1 3 70 1.271994 1.137524 0.13447 0.9264095990001806 211.578125 2026-11-02T00:31:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIXP4QG5B_10000.chr19.cool --window 5 --scales 4 --out gm12878/insulation/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-peaks chromosomix 0.19.0 at 997e59c peaks peaks 1 3 71 37.073521 35.554082 1.519439 34.83471513599943 237.21875 2026-11-02T00:31:43 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/ENCFF734CUT.chr19.bw --replicate data/ENCFF644EEX.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out gm12878/yapc/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw chromosomix 0.19.0 at 997e59c APA, raw APA 1 3 72 0.681446 0.58843 0.093016 0.4644353299991053 211.578125 2026-11-02T00:32:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw-every chromosomix 0.19.0 at 997e59c APA, raw, every pair APA 1 3 73 1.062087 0.92684 0.135247 0.7706814620014484 226.54296875 2026-11-02T00:32:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw-every 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-signal chromosomix 0.19.0 at 997e59c metaplot, CTCF and ATAC-seq, ±2 kb metaplot, signal 1 3 74 1.080033 0.882836 0.19719699999999998 0.8263498689993867 265.42578125 2026-11-02T00:32:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/ENCFF734CUT.chr19.bw --tracks data/ENCFF644EEX.chr19.bw --tracks data/ENCFF487LOB.chr19.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 2000 --step 50 --band none --out gm12878/metaplot/app-signal 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-insulation chromosomix 0.19.0 at 997e59c metaplot, insulation at four scales, ±500 kb metaplot, insulation 1 3 75 1.143943 0.9666119999999999 0.177331 0.9405553890010196 211.578125 2026-11-02T00:32:20 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 500000 --step 10000 --band none --out gm12878/metaplot/app-insulation 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-cooltools-insulation cooltools 0.7.1 insulation, four scales insulation 4 3 76 5.860705 5.312856 0.547849 5.283329173000311 806.4736328125 2026-11-02T00:32:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation_scales.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/insulation/cooltools.tsv 4 50000 100000 200000 400000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 peaks, seed 0 peaks 1 3 77 79.936888 76.816385 3.120503 80.06800780199956 1596.26953125 2026-11-02T00:32:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 gm12878/yapc/seed0/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw coolpuppy 1.1.0 APA, raw APA 4 3 78 3.078632 2.582794 0.495838 2.5954015540010005 1063.484375 2026-11-02T00:33:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw.tsv 4 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw-every coolpuppy 1.1.0 APA, raw, every pair APA 4 3 79 3.2817679999999996 2.785884 0.495884 2.7974225199996 1091.671875 2026-11-02T00:33:49 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw-every.tsv 4 --mindist 0 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-signal deepTools 4.0.0 computeMatrix metaplot, signal 4 3 80 0.807874 0.741885 0.06598899999999999 0.4657457390003401 211.578125 2026-11-02T00:33:52 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw data/ENCFF487LOB.chr19.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 2000 -a 2000 --binSize 50 -p 4 -o gm12878/metaplot/deeptools-signal.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-signal deepTools 4.0.0 plotProfile metaplot, signal 1 3 81 0.9956419999999999 0.944661 0.050981 0.6931190960003732 211.578125 2026-11-02T00:33:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-profile.png --outFileNameData gm12878/metaplot/deeptools-signal-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-signal deepTools 4.0.0 plotHeatmap metaplot, signal 1 3 82 1.373331 1.272381 0.10095 1.0654784920006932 211.578125 2026-11-02T00:33:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-signal-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-insulation deepTools 4.0.0 computeMatrix metaplot, insulation 4 3 83 39.563361 29.922315 9.641046 11.040837092999936 945.79296875 2026-11-02T00:33:54 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 500000 -a 500000 --binSize 10000 -p 4 -o gm12878/metaplot/deeptools-insulation.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-insulation deepTools 4.0.0 plotProfile metaplot, insulation 1 3 84 1.093963 1.036124 0.057838999999999995 0.8037788300007378 211.578125 2026-11-02T00:34:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-profile.png --outFileNameData gm12878/metaplot/deeptools-insulation-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-insulation deepTools 4.0.0 plotHeatmap metaplot, insulation 1 3 85 1.588403 1.510384 0.07801899999999999 1.2810999430002994 211.578125 2026-11-02T00:34:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-insulation-heatmap.bed 25 Pairs statistics yeast Hi-C contact list, deduplicated pairstats chromosomix 0.19.0 at 997e59c 1 3 86 66.76688899999999 45.098963 21.667926 60.250704517000486 216.09375 2026-11-02T00:34:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix stats data/CH128.pairs.gz --out pairstats/app 25 Pairs statistics yeast Hi-C contact list, deduplicated pairtools-stats pairtools 1.1.2 1 3 87 82.710836 73.337542 9.373294 73.56733143800011 307.859375 2026-11-02T00:35:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins restriction chromosomix 0.19.0 at 997e59c 1 3 88 1.1399249999999999 0.641347 0.49857799999999997 1.0280607679997047 211.578125 2026-11-02T00:36:21 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix restriction restriction/CH128.5000.cool --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-sites 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins bioframe-digest bioframe, Biopython 0.8.0, 1.88 1 3 89 1.224986 1.151868 0.073118 0.9204141000009258 211.578125 2026-11-02T00:36:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bioframe_digest.py data/R64-1-1.fa DpnII 5000 restriction/digest -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc chromosomix 0.19.0 at 997e59c 1 3 90 139.603646 97.510931 42.092715 123.92695517599896 317.91015625 2026-11-02T00:36:23 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix pairsqc data/CH128.pairs.gz --bin-size 5000 --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-pairsqc 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooler-cload cooler 0.10.4 1 3 91 44.772244 43.652242 1.120002 44.55075772700002 2338.89453125 2026-11-02T00:38:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 data/R64-1-1.chrom.sizes:5000 data/CH128.pairs.gz restriction/CH128.5000.cool 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-top pairtools 1.1.2 1 3 92 338.387198 328.771572 9.615626 205.3043475480008 211.578125 2026-11-02T00:39:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags.bed data/CH128.pairs.gz -o restriction/CH128.restricted.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-bottom pairtools 1.1.2 1 3 93 335.53262 326.05368 9.47894 204.14918493500045 211.578125 2026-11-02T00:42:37 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags-bottom.bed data/CH128.pairs.gz -o restriction/CH128.restricted-bottom.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb restriction-reference pandas 2.3.3 1 3 94 75.95396199999999 73.762992 2.19097 76.7059001029993 845.515625 2026-11-02T00:46:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/restriction_reference.py data/R64-1-1.fa DpnII restriction/CH128.restricted.pairs.gz restriction/CH128.restricted-bottom.pairs.gz restriction/pairtools -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooltools-coverage-sites cooltools 0.7.1 4 3 95 2.0662779999999996 1.7866339999999998 0.279644 1.4121489360004489 296.5546875 2026-11-02T00:47:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage_sites.py restriction/CH128.5000.cool restriction/digest.sites.tsv restriction/coverage 4 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc-pairtools-stats pairtools 1.1.2 1 3 96 79.520157 70.332438 9.187719 70.14251482299915 308.3046875 2026-11-02T00:47:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-raw chromosomix 0.19.0 at 997e59c raw raw 1 3 97 5.948639 5.227592 0.721047 6.617113076999885 518.84765625 2026-11-02T00:48:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --no-balance --out arrowhead/app-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 3 98 5.93175 5.242501 0.689249 6.202592236999408 531.375 2026-11-02T00:48:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --out arrowhead/app-balanced 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-raw Juicer Tools 1.22.01, on Java 21.0.13 raw raw 1 3 99 40.335128000000005 36.005732 4.329396 20.17414610599917 3510.1875 2026-11-02T00:48:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k NONE --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-balanced Juicer Tools 1.22.01, on Java 21.0.13 balanced balanced 1 3 100 42.188793 37.919785 4.269008 21.313366738000695 3744.6875 2026-11-02T00:49:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k KR --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-balanced 29 Map report yeast Micro-C, every stored resolution mapreport chromosomix 0.19.0 at 997e59c 1 3 101 3.349878 3.099091 0.250787 2.792969706999429 233.9921875 2026-11-02T00:49:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix mapreport data/GSE151553_A364_merged.mcool::/resolutions/800 --out mapreport/app 29 Map report yeast Micro-C, every stored resolution map-resolution cooler 0.10.4 1 3 102 5.680362 5.287933 0.392429 5.408986713999184 861.234375 2026-11-02T00:49:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/map_resolution.py data/GSE151553_A364_merged.mcool mapreport/cooler.tsv 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb cooltools-insulation cooltools 0.7.1 4 4 1 11.40042 10.613827 0.786593 4.9719929180009785 890.28515625 2026-11-02T00:49:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 insulation/cooltools.tsv 4 1 Diamond insulation mouse Hi-C, 10 kb, window 100 kb insulation chromosomix 0.19.0 at 997e59c 1 4 0 4.797365999999999 4.335925 0.461441 3.8198772550003923 301.515625 2026-11-02T00:49:37 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --window 10 --out insulation/app 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb domaincaller-di domaincaller 0.1.0 1 4 3 2.7520709999999995 2.5891219999999997 0.16294899999999998 2.471815016999244 258.328125 2026-11-02T00:49:41 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/domaincaller_di.py data/4DNFIOZ1TRUS.mcool::/resolutions/50000 di/domaincaller.npy 2 Directionality index mouse Hi-C, 50 kb, window 2 Mb di chromosomix 0.19.0 at 997e59c 1 4 2 2.288556 2.127461 0.161095 1.762578404001033 211.578125 2026-11-02T00:49:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix di data/4DNFIOZ1TRUS.mcool::/resolutions/50000 --window 40 --out di/app 3 Compartments mouse Hi-C, 100 kb, GC-phased cooltools-eigs cooltools 0.7.1 1 4 5 14.442706000000001 13.931765 0.510941 7.476969645000281 559.93359375 2026-11-02T00:49:45 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_eigs_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 compartments/gc.tsv compartments/cooltools 3 Compartments mouse Hi-C, 100 kb, GC-phased compartments chromosomix 0.19.0 at 997e59c 1 4 4 5.708646 5.375214 0.333432 4.127358195999477 277.796875 2026-11-02T00:49:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix compartments data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --components 3 --phaseTrack compartments/gc.bedGraph --out compartments/app 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-yeast cooltools 0.7.1 yeast 800 bp yeast 800 bp 4 4 8 2.956369 2.484495 0.47187399999999996 2.3058392359998834 956.71484375 2026-11-02T00:49:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/GSE151553_A364_merged.mcool::/resolutions/800 ps/yeast-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb cooltools-expected-mouse cooltools 0.7.1 mouse 10 kb mouse 10 kb 4 4 9 25.000401000000004 16.455442 8.544959 8.930346699999063 10508.8046875 2026-11-02T00:49:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_expected_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 ps/mouse-cooltools.tsv 4 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-yeast chromosomix 0.19.0 at 997e59c yeast 800 bp yeast 800 bp 1 4 6 0.6941299999999999 0.6081059999999999 0.08602399999999999 0.5267020740011503 211.578125 2026-11-02T00:50:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/GSE151553_A364_merged.mcool::/resolutions/800 --quantity expected --scope file --out ps/yeast 4 P(s) yeast Micro-C 800 bp; mouse Hi-C 10 kb expected-mouse chromosomix 0.19.0 at 997e59c mouse 10 kb mouse 10 kb 1 4 7 2.8209090000000003 2.5054790000000002 0.31543 2.36175101399931 236.4609375 2026-11-02T00:50:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix expected data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --quantity expected --scope file --out ps/mouse 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 seed 0 seed 0 1 4 11 61.905989 58.629408 3.276581 62.05529550900064 1667.7578125 2026-11-02T00:50:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 yapc/seed0/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 5 Peak calling (yapc, IDR) mouse ATAC-seq, 2 replicates, chr19 peaks chromosomix 0.19.0 at 997e59c 1 4 10 20.425131999999998 18.772719 1.6524130000000001 18.533951352001168 277.39453125 2026-11-02T00:51:13 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/4DNFIIY4QW2D.chr19.bw --replicate data/4DNFITBRHVZE.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out yapc/app 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosight 1.6.3 4 4 13 31.022982 29.633321 1.389661 10.67700252099894 705.904296875 2026-11-02T00:51:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight detect --pattern loops --threads 4 data/GSE151553_A364_merged.mcool::/resolutions/800 loops/chromosight/loops 6 Loops (chromosight) yeast Micro-C, 800 bp chromosight chromosomix 0.19.0 at 997e59c 1 4 12 6.162838 5.9394089999999995 0.223429 5.084581745000833 268.97265625 2026-11-02T00:51:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix chromosight data/GSE151553_A364_merged.mcool::/resolutions/800 --pattern loops --out loops/app 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep hicrep 0.2.6 3 maps, 3 pairs 3 maps, 3 pairs 1 4 15 5.445819 5.187846 0.257973 5.182499776999975 259.03515625 2026-11-02T00:51:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/hicrep_scc.py hicrep/hicrep.tsv chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ 4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000 4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000 4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000 7 Reproducibility (HiCRep) chicken Hi-C, 3 maps, 100 kb, raw counts hicrep chromosomix 0.19.0 at 997e59c 3 maps, 3 pairs 3 maps, 3 pairs 1 4 14 3.952611 3.732071 0.22053999999999999 3.1377818809996825 249.5 2026-11-02T00:51:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix hicrep data/4DNFIH8L6WON.mcool::/resolutions/100000 --against data/4DNFITBCUX56.mcool::/resolutions/100000 --against data/4DNFIIML46E5.mcool::/resolutions/100000 --maxDistance 50 --smooth 1 --no-balance --sequences chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ --out hicrep/app 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads pastis-seed0 pastis 0.5.0 seed 0 seed 0 1 4 17 80.716253 77.590012 3.126241 28.814485798000533 359.4453125 2026-11-02T00:51:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed0.npy 0 8 3D model (pastis-NB) yeast Micro-C, 12.8 kb, 905 beads reconstruct3d-seed0 chromosomix 0.19.0 at 997e59c seed 0 seed 0 1 4 16 5.7553339999999995 5.611927 0.143407 5.4594455789992935 211.578125 2026-11-02T00:52:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 0 --out pastis/app-seed0 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-raw cooltools 0.7.1 raw raw 4 4 20 5.730365 4.969101 0.7612639999999999 2.632452067000486 1592.0400390625 2026-11-02T00:52:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-raw.tsv 4 9 Coverage mouse Hi-C, 10 kb, raw and balanced cooltools-coverage-balanced cooltools 0.7.1 balanced balanced 4 4 21 6.281079 5.51943 0.761649 2.9933810040001845 1433.7890625 2026-11-02T00:52:33 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-balanced.tsv 4 weight 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-raw chromosomix 0.19.0 at 997e59c raw raw 1 4 18 3.817407 3.437476 0.37993099999999996 3.1493642530003854 353.75 2026-11-02T00:52:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --out coverage/raw 9 Coverage mouse Hi-C, 10 kb, raw and balanced coverage-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 4 19 4.043054 3.5741199999999997 0.46893399999999996 3.3430035959991073 275.34765625 2026-11-02T00:52:39 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --balance --out coverage/balanced 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome cooltools-virtual4c-Sox2 cooltools 0.7.1 Sox2 Sox2 4 4 23 6.753907 6.277903 0.476004 2.8827088570014894 525.171875 2026-11-02T00:52:42 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr3:34650000-34660000 virtual4c/cooltools-Sox2.tsv 4 10 Virtual 4C mouse Hi-C, 10 kb, three viewpoints, whole genome fourc-Sox2 chromosomix 0.19.0 at 997e59c Sox2 Sox2 1 4 22 1.2325490000000001 1.075118 0.157431 0.9496847280006477 245.76953125 2026-11-02T00:52:45 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr3:34,650,001-34,660,000 --no-cis --out virtual4c/Sox2 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw coolpuppy 1.1.0 raw raw 4 4 28 9.086791 8.17741 0.909381 3.598183744999915 877.8994140625 2026-11-02T00:52:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw.tsv 4 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-raw-every coolpuppy 1.1.0 raw, every loop raw, every loop 4 4 29 8.888819 7.996926 0.8918929999999999 3.5364537320001546 820.7958984375 2026-11-02T00:52:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw-every.tsv 4 --mindist 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-local coolpuppy 1.1.0 on the diagonal, raw on the diagonal, raw 4 4 30 9.245503999999999 8.345467 0.900037 3.6577014640006382 885.6337890625 2026-11-02T00:52:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local.tsv 4 --local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops coolpuppy-controls-seed0 coolpuppy 1.1.0 controls, seed 0 controls 4 4 31 8.716603 7.875328 0.841275 3.41179224500047 885.9599609375 2026-11-02T00:52:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed0.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 0 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw chromosomix 0.19.0 at 997e59c raw raw 1 4 24 1.2979990000000001 1.164352 0.133647 0.8959176360003767 211.578125 2026-11-02T00:53:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/raw 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-raw-every chromosomix 0.19.0 at 997e59c raw, every loop raw, every loop 1 4 25 1.985062 1.814392 0.17067 1.4098684770015097 211.578125 2026-11-02T00:53:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/raw-every 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-local chromosomix 0.19.0 at 997e59c on the diagonal, raw on the diagonal, raw 1 4 26 2.193577 1.990339 0.203238 1.515949107000779 211.578125 2026-11-02T00:53:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm none --mode fixed --window 5 --minDiag 2 --out apa/local 11 Aggregate peak analysis mouse Hi-C, 10 kb, 2,515 loops apa-controls-seed1 chromosomix 0.19.0 at 997e59c controls, seed 1 controls 1 4 27 2.352423 2.195863 0.15656 1.6859022730004654 211.578125 2026-11-02T00:53:04 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 1 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed1 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops chromosight-quantify chromosight 1.6.3 4 4 33 83.32092800000001 80.013851 3.307077 26.66326672300056 1476.7509765625 2026-11-02T00:53:06 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosight quantify --pattern loops --threads 4 apa/loops.bedpe data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chromosight-quantify/quantify 12 APA, chromosight's score mouse Hi-C, 10 kb, 2,515 loops apa-chromosight chromosomix 0.19.0 at 997e59c 1 4 32 5.063338 4.85182 0.21151799999999998 3.685627824999756 236.1484375 2026-11-02T00:53:32 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm chromosight --out chromosight-quantify/app 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boosthic-chr1 Boost-HiC a615aff chr1, 1,955 bins chr1, 1,955 bins 1 4 35 20.034602 19.814562 0.22003999999999999 19.54088644100011 462.484375 2026-11-02T00:53:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr1 boost-hic/boosthic-chr1 13 Boost-HiC mouse Hi-C, 100 kb, chr19, chr11, chr1 boost-chr1 chromosomix 0.19.0 at 997e59c chr1, 1,955 bins chr1, 1,955 bins 1 4 34 3.643352 3.173178 0.470174 3.4310187060000317 651.9921875 2026-11-02T00:53:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr1 --out boost-hic/chr1 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix deepTools 4.0.0 computeMatrix TSS 4 4 38 3.525542 3.034797 0.490745 4.627280960999997 211.578125 2026-11-02T00:53:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile deepTools 4.0.0 plotProfile TSS 1 4 39 1.833713 1.733784 0.09992899999999999 1.533619654001086 219.35546875 2026-11-02T00:54:04 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools.mat.gz -out metaplot/deeptools-profile.png --outFileNameData metaplot/deeptools-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb computematrix-two deepTools 4.0.0 computeMatrix TSS, two tracks 4 4 40 6.314952999999999 5.618643 0.69631 4.641741974000979 244.82421875 2026-11-02T00:54:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/4DNFIIY4QW2D.bw data/4DNFITBRHVZE.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools-two.mat.gz 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotprofile-two deepTools 4.0.0 plotProfile TSS, two tracks 1 4 41 2.5574239999999997 2.438312 0.119112 2.251534867000373 262.69140625 2026-11-02T00:54:10 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-profile.png --outFileNameData metaplot/deeptools-two-profile.tab 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb plotheatmap-two deepTools 4.0.0 plotHeatmap TSS, two tracks 1 4 42 3.202076 2.989071 0.213005 2.896810917000039 487.203125 2026-11-02T00:54:12 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-heatmap.png --outFileSortedRegions metaplot/deeptools-two-heatmap.bed 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot chromosomix 0.19.0 at 997e59c TSS 1 4 36 4.249073 3.563073 0.6859999999999999 3.5059629949992086 380.32421875 2026-11-02T00:54:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app 14 Metaplot mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb metaplot-two chromosomix 0.19.0 at 997e59c TSS, two tracks 1 4 37 7.4820210000000005 6.320185 1.161836 6.1019497029992635 434.0 2026-11-02T00:54:19 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --tracks data/4DNFITBRHVZE.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app-two 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 bedtools-overlap bedtools 2.31.1 1 4 44 41.17769 27.933629 13.244061 36.94745343500108 211.578125 2026-11-02T00:54:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bedtools_overlap.py yapc/seed0/yapc_0.05.bed overlap/promoters.bed overlap/mm10.genome 1000 overlap/bedtools 15 Interval overlap ATAC-seq peaks (§ 5) and promoters, chr19 overlap chromosomix 0.19.0 at 997e59c 1 4 43 1.109695 1.077325 0.032369999999999996 1.0399661930005095 211.578125 2026-11-02T00:55:02 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix overlap --sequence data/mm10.fa --features yapc/seed0/yapc_0.05.bed --features overlap/promoters.bed --a yapc/seed0/yapc_0.05.bed --b overlap/promoters.bed --shuffle --iterations 1000 --seed 1 --out overlap/app 16 Base composition mm10, 10 kb bins composition bioframe, Biopython 0.8.0, 1.88 1 4 46 40.522467999999996 33.936679 6.585789 43.90299803900052 507.56640625 2026-11-02T00:55:03 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/composition.py data/mm10.fa 10000 composition/reference.tsv 16 Base composition mm10, 10 kb bins composition chromosomix 0.19.0 at 997e59c 1 4 45 3.799408 3.250852 0.5485559999999999 3.095444171998679 286.76171875 2026-11-02T00:55:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix composition --sequence data/mm10.fa --resolution 10000 --out composition/app 17 Motif search mm10 chr19, two motifs, both strands seqkit-TGACTCA seqkit 2.3.0 TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 4 4 49 19.472805 17.81078 1.6620249999999999 19.257685849001064 3942.4375 2026-11-02T00:55:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -m 1 -p TGACTCA --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-TGACTCA.bed 17 Motif search mm10 chr19, two motifs, both strands seqkit-WGATAR seqkit 2.3.0 WGATAR WGATAR 4 4 50 6.33782 6.163728 0.174092 6.052010822000739 343.359375 2026-11-02T00:56:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c seqkit locate -i -d -p WGATAR --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-WGATAR.bed 17 Motif search mm10 chr19, two motifs, both strands motif-TGACTCA chromosomix 0.19.0 at 997e59c TGACTCA, ≤ 1 mismatch TGACTCA, ≤ 1 mismatch 1 4 47 5.125579999999999 2.6302019999999997 2.495378 5.06970054500016 359.27734375 2026-11-02T00:56:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern TGACTCA --mismatches 1 --out motif/TGACTCA 17 Motif search mm10 chr19, two motifs, both strands motif-WGATAR chromosomix 0.19.0 at 997e59c WGATAR WGATAR 1 4 48 4.121091 2.117411 2.00368 4.005326415001036 306.01171875 2026-11-02T00:56:20 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix motif --sequence data/mm10.chr19.fa --pattern WGATAR --mismatches 0 --out motif/WGATAR 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-100 deepTools 4.0.0 100 bp, the windows 100 bp windows 4 4 57 189.588457 184.748684 4.839773 50.73142424099933 305.69140625 2026-11-02T00:56:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 100 -p 4 -o trackcorr/deeptools-100.npz --outRawCounts trackcorr/deeptools-100.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-pearson deepTools 4.0.0 100 bp, pearson 100 bp windows 1 4 58 1.7656159999999999 1.6066509999999998 0.158965 1.154249928000354 270.81640625 2026-11-02T00:57:15 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c pearson -p heatmap -o trackcorr/deeptools-100-pearson.png --outFileCorMatrix trackcorr/deeptools-100-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-100-spearman deepTools 4.0.0 100 bp, spearman 100 bp windows 1 4 59 2.220507 2.048778 0.171729 1.6082267260007939 269.96484375 2026-11-02T00:57:16 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-100.npz -c spearman -p heatmap -o trackcorr/deeptools-100-spearman.png --outFileCorMatrix trackcorr/deeptools-100-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-1000 deepTools 4.0.0 1,000 bp, the windows 1,000 bp windows 4 4 60 17.577645 17.093361 0.484284 4.741374171000643 211.578125 2026-11-02T00:57:18 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 1000 -p 4 -o trackcorr/deeptools-1000.npz --outRawCounts trackcorr/deeptools-1000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-pearson deepTools 4.0.0 1,000 bp, pearson 1,000 bp windows 1 4 61 1.3935170000000001 1.273473 0.120044 0.7760645390007994 211.578125 2026-11-02T00:57:22 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c pearson -p heatmap -o trackcorr/deeptools-1000-pearson.png --outFileCorMatrix trackcorr/deeptools-1000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-1000-spearman deepTools 4.0.0 1,000 bp, spearman 1,000 bp windows 1 4 62 1.46027 1.3562509999999999 0.104019 0.8414977009997529 211.578125 2026-11-02T00:57:23 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-1000.npz -c spearman -p heatmap -o trackcorr/deeptools-1000-spearman.png --outFileCorMatrix trackcorr/deeptools-1000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows multibigwigsummary-10000 deepTools 4.0.0 10,000 bp, the windows 10,000 bp windows 4 4 63 2.282069 2.182387 0.09968199999999999 0.70011165699907 211.578125 2026-11-02T00:57:24 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 10000 -p 4 -o trackcorr/deeptools-10000.npz --outRawCounts trackcorr/deeptools-10000.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-pearson deepTools 4.0.0 10,000 bp, pearson 10,000 bp windows 1 4 64 1.3582070000000002 1.265125 0.093082 0.7405605669991928 211.578125 2026-11-02T00:57:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c pearson -p heatmap -o trackcorr/deeptools-10000-pearson.png --outFileCorMatrix trackcorr/deeptools-10000-pearson.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows plotcorrelation-10000-spearman deepTools 4.0.0 10,000 bp, spearman 10,000 bp windows 1 4 65 1.415519 1.333778 0.081741 0.7963063349998265 211.578125 2026-11-02T00:57:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotCorrelation -in trackcorr/deeptools-10000.npz -c spearman -p heatmap -o trackcorr/deeptools-10000-spearman.png --outFileCorMatrix trackcorr/deeptools-10000-spearman.tab 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-pearson chromosomix 0.19.0 at 997e59c 100 bp, pearson 100 bp windows 1 4 51 0.727773 0.632672 0.09510099999999999 0.5535303950000525 211.578125 2026-11-02T00:57:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method pearson --out trackcorr/app-100-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-100-spearman chromosomix 0.19.0 at 997e59c 100 bp, spearman 100 bp windows 1 4 52 1.5448629999999999 1.358363 0.1865 1.2887288329984585 326.3515625 2026-11-02T00:57:27 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method spearman --out trackcorr/app-100-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-pearson chromosomix 0.19.0 at 997e59c 1,000 bp, pearson 1,000 bp windows 1 4 53 0.7318119999999999 0.6580159999999999 0.073796 0.4976897460001055 211.578125 2026-11-02T00:57:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method pearson --out trackcorr/app-1000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-1000-spearman chromosomix 0.19.0 at 997e59c 1,000 bp, spearman 1,000 bp windows 1 4 54 0.8248300000000001 0.750298 0.074532 0.5770269859986001 211.578125 2026-11-02T00:57:28 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method spearman --out trackcorr/app-1000-spearman 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-pearson chromosomix 0.19.0 at 997e59c 10,000 bp, pearson 10,000 bp windows 1 4 55 0.7047599999999999 0.6249009999999999 0.079859 0.483756383000582 211.578125 2026-11-02T00:57:29 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method pearson --out trackcorr/app-10000-pearson 18 Track correlation mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows trackcorr-10000-spearman chromosomix 0.19.0 at 997e59c 10,000 bp, spearman 10,000 bp windows 1 4 56 0.757687 0.676507 0.08118 0.5062799590014038 211.578125 2026-11-02T00:57:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method spearman --out trackcorr/app-10000-spearman 19 Loop calling mouse Hi-C, 10 kb, every chromosome cooltools-dots cooltools 0.7.1 4 4 67 548.461808 517.487653 30.974155 153.781755031001 11315.4677734375 2026-11-02T00:57:30 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_dots.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 loopcalling/cooltools.tsv 4 19 Loop calling mouse Hi-C, 10 kb, every chromosome loops chromosomix 0.19.0 at 997e59c 1 4 66 24.592134 23.406258 1.185876 21.232289690999096 456.22265625 2026-11-02T01:00:04 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix loops data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --out loopcalling/app 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches pybigwig-groupsignal-entries pyBigWig, SciPy 0.3.26, 1.16.3 one value per entry one value per entry 1 4 69 1.4828459999999999 1.354946 0.12789999999999999 0.8751214300009451 211.578125 2026-11-02T01:00:25 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 0 groupsignal/reference-entries data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw 23 Signal by group mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches groupsignal-entries chromosomix 0.19.0 at 997e59c one value per entry one value per entry 1 4 68 0.648018 0.5584629999999999 0.089555 0.46242375299880223 211.578125 2026-11-02T01:00:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --out groupsignal/app-entries 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-cooltools-insulation cooltools 0.7.1 insulation, four scales insulation 4 4 76 5.595059 5.08528 0.509779 4.96346548800102 806.6611328125 2026-11-02T01:00:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_insulation_scales.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/insulation/cooltools.tsv 4 50000 100000 200000 400000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-yapc-seed0 yapc 0.1 0.1, with idr 2.0.3 peaks, seed 0 peaks 1 4 77 78.879847 75.718615 3.161232 78.8915170299988 1596.57421875 2026-11-02T01:00:31 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c yapc-env/bin/python ../../scripts/yapc_idr.py 0 gm12878/yapc/seed0/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw coolpuppy 1.1.0 APA, raw APA 4 4 78 3.0423679999999997 2.56059 0.481778 2.5729700709998724 1088.84765625 2026-11-02T01:01:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw.tsv 4 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-coolpuppy-raw-every coolpuppy 1.1.0 APA, raw, every pair APA 4 4 79 3.200841 2.699261 0.50158 2.727045976000227 1091.60546875 2026-11-02T01:01:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw-every.tsv 4 --mindist 0 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-signal deepTools 4.0.0 computeMatrix metaplot, signal 4 4 80 0.738676 0.684991 0.053685 0.423400526999103 211.578125 2026-11-02T01:01:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw data/ENCFF487LOB.chr19.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 2000 -a 2000 --binSize 50 -p 4 -o gm12878/metaplot/deeptools-signal.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-signal deepTools 4.0.0 plotProfile metaplot, signal 1 4 81 0.918807 0.85375 0.065057 0.6149585590010247 211.578125 2026-11-02T01:01:56 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-profile.png --outFileNameData gm12878/metaplot/deeptools-signal-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-signal deepTools 4.0.0 plotHeatmap metaplot, signal 1 4 82 1.317921 1.2269269999999999 0.09099399999999999 1.0087520760007465 211.578125 2026-11-02T01:01:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-signal-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-computematrix-insulation deepTools 4.0.0 computeMatrix metaplot, insulation 4 4 83 38.127815 29.273702 8.854113 10.790496228999473 945.82421875 2026-11-02T01:01:58 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c computeMatrix reference-point -S gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 500000 -a 500000 --binSize 10000 -p 4 -o gm12878/metaplot/deeptools-insulation.mat.gz 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotprofile-insulation deepTools 4.0.0 plotProfile metaplot, insulation 1 4 84 1.0688739999999999 0.998883 0.069991 0.7602111609994608 211.578125 2026-11-02T01:02:08 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotProfile -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-profile.png --outFileNameData gm12878/metaplot/deeptools-insulation-profile.tab 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-plotheatmap-insulation deepTools 4.0.0 plotHeatmap metaplot, insulation 1 4 85 1.609136 1.5182419999999999 0.090894 1.3025579389995983 211.578125 2026-11-02T01:02:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c plotHeatmap -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-insulation-heatmap.bed 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-insulation chromosomix 0.19.0 at 997e59c insulation, four scales insulation 1 4 70 1.287202 1.15698 0.130222 0.9333155570002418 211.578125 2026-11-02T01:02:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix insulation data/4DNFIXP4QG5B_10000.chr19.cool --window 5 --scales 4 --out gm12878/insulation/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-peaks chromosomix 0.19.0 at 997e59c peaks peaks 1 4 71 37.20881 35.650871 1.557939 34.87894670299829 221.33203125 2026-11-02T01:02:11 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix peaks --signal data/ENCFF734CUT.chr19.bw --replicate data/ENCFF644EEX.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out gm12878/yapc/app 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw chromosomix 0.19.0 at 997e59c APA, raw APA 1 4 72 0.695492 0.587104 0.108388 0.4708110840001609 211.578125 2026-11-02T01:02:46 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-apa-raw-every chromosomix 0.19.0 at 997e59c APA, raw, every pair APA 1 4 73 1.06933 0.930639 0.13869099999999998 0.7755896440012293 211.578125 2026-11-02T01:02:47 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw-every 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-signal chromosomix 0.19.0 at 997e59c metaplot, CTCF and ATAC-seq, ±2 kb metaplot, signal 1 4 74 1.0765959999999999 0.8909039999999999 0.185692 0.8220220420007536 259.05078125 2026-11-02T01:02:48 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks data/ENCFF734CUT.chr19.bw --tracks data/ENCFF644EEX.chr19.bw --tracks data/ENCFF487LOB.chr19.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 2000 --step 50 --band none --out gm12878/metaplot/app-signal 24 CTCF sites in GM12878 (Fig. 2) GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19 gm-metaplot-insulation chromosomix 0.19.0 at 997e59c metaplot, insulation at four scales, ±500 kb metaplot, insulation 1 4 75 1.13583 0.9349069999999999 0.200923 0.9364458170002763 211.578125 2026-11-02T01:02:48 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix metaplot --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 500000 --step 10000 --band none --out gm12878/metaplot/app-insulation 25 Pairs statistics yeast Hi-C contact list, deduplicated pairtools-stats pairtools 1.1.2 1 4 87 79.270162 69.932073 9.338089 70.17546795999988 305.76171875 2026-11-02T01:02:49 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 25 Pairs statistics yeast Hi-C contact list, deduplicated pairstats chromosomix 0.19.0 at 997e59c 1 4 86 65.019727 43.623803 21.395924 59.11723865900058 290.57421875 2026-11-02T01:04:00 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix stats data/CH128.pairs.gz --out pairstats/app 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins bioframe-digest bioframe, Biopython 0.8.0, 1.88 1 4 89 1.1051490000000002 1.022512 0.082637 0.7991526289988542 211.578125 2026-11-02T01:04:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/bioframe_digest.py data/R64-1-1.fa DpnII 5000 restriction/digest -2 26 Restriction sites yeast R64-1-1, DpnII, 5 kb bins restriction chromosomix 0.19.0 at 997e59c 1 4 88 1.1135769999999998 0.6176699999999999 0.495907 1.0529591679987789 211.578125 2026-11-02T01:04:59 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix restriction restriction/CH128.5000.cool --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-sites 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooler-cload cooler 0.10.4 1 4 91 43.519767 42.351853 1.167914 43.2675186230008 2339.2734375 2026-11-02T01:05:01 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 data/R64-1-1.chrom.sizes:5000 data/CH128.pairs.gz restriction/CH128.5000.cool 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-top pairtools 1.1.2 1 4 92 340.018857 330.12004 9.898817 205.0218896869992 211.578125 2026-11-02T01:05:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags.bed data/CH128.pairs.gz -o restriction/CH128.restricted.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairtools-restrict-bottom pairtools 1.1.2 1 4 93 340.586418 331.101369 9.485049 206.72571311299907 211.578125 2026-11-02T01:09:09 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools restrict -f restriction/digest.frags-bottom.bed data/CH128.pairs.gz -o restriction/CH128.restricted-bottom.pairs.gz 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb restriction-reference pandas 2.3.3 1 4 94 75.399967 73.302024 2.097943 75.80734879600095 851.9765625 2026-11-02T01:12:36 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/restriction_reference.py data/R64-1-1.fa DpnII restriction/CH128.restricted.pairs.gz restriction/CH128.restricted-bottom.pairs.gz restriction/pairtools -2 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb cooltools-coverage-sites cooltools 0.7.1 4 4 95 2.0793619999999997 1.7956159999999999 0.283746 1.4252364589992794 296.6953125 2026-11-02T01:13:51 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/cooltools_coverage_sites.py restriction/CH128.5000.cool restriction/digest.sites.tsv restriction/coverage 4 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc-pairtools-stats pairtools 1.1.2 1 4 96 81.142101 71.822707 9.319394 71.57866247199854 307.95703125 2026-11-02T01:13:53 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats 27 Pairs QC § 25's contact list against § 26's DpnII sites, 5 kb pairsqc chromosomix 0.19.0 at 997e59c 1 4 90 135.191787 92.213983 42.977804 122.90286227999968 320.34765625 2026-11-02T01:15:05 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix pairsqc data/CH128.pairs.gz --bin-size 5000 --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-pairsqc 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-raw Juicer Tools 1.22.01, on Java 21.0.13 raw raw 1 4 99 33.066731 31.50133 1.565401 18.16196033400047 2654.9609375 2026-11-02T01:17:07 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k NONE --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR juicer-arrowhead-balanced Juicer Tools 1.22.01, on Java 21.0.13 balanced balanced 1 4 100 35.718066 33.659916 2.05815 18.861309870000696 3946.84375 2026-11-02T01:17:26 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k KR --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-balanced 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-raw chromosomix 0.19.0 at 997e59c raw raw 1 4 97 5.773833 5.161564 0.612269 5.933062849000635 514.078125 2026-11-02T01:17:44 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --no-balance --out arrowhead/app-raw 28 TAD annotation K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR arrowhead-balanced chromosomix 0.19.0 at 997e59c balanced balanced 1 4 98 5.951036 5.206653 0.744383 6.242496049999318 566.65625 2026-11-02T01:17:50 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --out arrowhead/app-balanced 29 Map report yeast Micro-C, every stored resolution map-resolution cooler 0.10.4 1 4 102 5.671262 5.263769 0.407493 5.397083691999796 861.18359375 2026-11-02T01:17:57 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c python ../../scripts/map_resolution.py data/GSE151553_A364_merged.mcool mapreport/cooler.tsv 29 Map report yeast Micro-C, every stored resolution mapreport chromosomix 0.19.0 at 997e59c 1 4 101 3.2760219999999998 3.00596 0.27006199999999997 2.7615611879991775 251.5078125 2026-11-02T01:18:02 AMD EPYC 9V45 96-Core Processor 4 16.8 Linux-7.0.0-1017-azure-x86_64-with-glibc2.39 v24.22.1 3.13.17 0.19.0 at 997e59c chromosomix mapreport data/GSE151553_A364_merged.mcool::/resolutions/800 --out mapreport/app