Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/e0f262157e8a427a2fa13efff9086b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/e0f262157e8a427a2fa13efff9086b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_27F-N1-BDNA-1_B23KGCJLT4_1/1136_27F-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_27F-N1-BDNA-1_B23KGCJLT4_1/1136_27F-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_27F-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_27F-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_27F-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_27F-N1-BDNA-1_B23KGCJLT4_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: 103187740 total, 70323 skipped (flags/unmapped)
Fragments: 51721622 total (51341468 tlen-paired, 3508 hash-paired, 482 singletons, 19455 discordant, 356709 orphans, 15682 too large [>5000 bp], 22141197 duplicates)
Reads: 111209113 total, 58525 skipped (flags/unmapped)
Fragments: 55746735 total (55361469 tlen-paired, 2769 hash-paired, 551 singletons, 13679 discordant, 368267 orphans, 12968 too large [>5000 bp], 23341479 duplicates)
Reads: 110967732 total, 64706 skipped (flags/unmapped)
Fragments: 55629399 total (55196044 tlen-paired, 5837 hash-paired, 421 singletons, 16594 discordant, 410503 orphans, 27576 too large [>5000 bp], 23859812 duplicates)
Reads: 122522302 total, 94718 skipped (flags/unmapped)
Fragments: 61538596 total (60522334 tlen-paired, 1910 hash-paired, 485 singletons, 198268 discordant, 815599 orphans, 83238 too large [>5000 bp], 26444296 duplicates)