Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_4DY-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_4DY-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_4DY-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_4DY-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai

Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 89571064 total, 65832 skipped (flags/unmapped)
Fragments: 44980420 total (44471046 tlen-paired, 10195 hash-paired, 6085 singletons, 8795 discordant, 484299 orphans, 17388 too large [>5000 bp], 10306589 duplicates)
Reads: 89001394 total, 75111 skipped (flags/unmapped)
Fragments: 44679569 total (44210869 tlen-paired, 9321 hash-paired, 6132 singletons, 9254 discordant, 443993 orphans, 8635 too large [>5000 bp], 10316739 duplicates)
Reads: 97411862 total, 67448 skipped (flags/unmapped)
Fragments: 48916731 total (48390491 tlen-paired, 10059 hash-paired, 6646 singletons, 6729 discordant, 502806 orphans, 10202 too large [>5000 bp], 11241820 duplicates)
Reads: 100703781 total, 119506 skipped (flags/unmapped)
Fragments: 50803724 total (49195282 tlen-paired, 9850 hash-paired, 6782 singletons, 320935 discordant, 1270875 orphans, 127242 too large [>5000 bp], 11561281 duplicates)