Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 12 threads; openjdk version "17.0.15" 2025-04-15; juicer.sh -d /storage3/artem/Trichoplax/Trih_2/ -p /storage3/artem/Trichoplax/Genome/file.chrom.sizes -z /storage3/artem/Trichoplax/Genome/H1pacbio_consensus.fa -t 12 -D /storage3/artem/Software/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Sequenced Read Pairs:  178,782,695
 Normal Paired: 112,013,802 (62.65%)
 Chimeric Paired: 25,142,972 (14.06%)
 Chimeric Ambiguous: 2,978,206 (1.67%)
 Unmapped: 38,647,715 (21.62%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 137,156,774 (76.72%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-03-29T17:30:04,221]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 110,134,143 (61.60%)
PCR Duplicates: 50,059 (0.03%)
Optical Duplicates: 26,972,572 (15.09%)
Library Complexity Estimate: 121,225,763,090
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 7,024,527 (3.93% / 6.38%)
Hi-C Contacts: 103,109,616 (57.67% / 93.62%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 4% - 89% - 4% - 4%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 77%
 Cis/all (FF and RR orient): 57.0%
Inter-chromosomal: 10,204,733  (5.71% / 9.27%)
Intra-chromosomal: 92,904,883  (51.97% / 84.36%)
Short Range (<20,000bp): 81,860,152  (45.79% / 74.33%)
Long Range (>20,000bp): 11,044,731  (6.18% / 10.03%)