Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_16G-T1-TDNA-1_B23KFCWLT4_1/1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b7a9ab8c91d9ab71924be15f412d22/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_16G-T1-TDNA-1_B23KFCWLT4_1/1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/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/3f/b7a9ab8c91d9ab71924be15f412d22/.command.run
==> 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: 1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-T1-TDNA-1_B23KFCWLT4_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: 323202247 total, 1128908 skipped (flags/unmapped)
Fragments: 161899006 total (159587511 tlen-paired, 99616 hash-paired, 1771 singletons, 257400 discordant, 1952708 orphans, 114903 too large [>5000 bp], 101412496 duplicates)
Reads: 344732505 total, 873746 skipped (flags/unmapped)
Fragments: 172663847 total (170790858 tlen-paired, 75180 hash-paired, 1807 singletons, 112018 discordant, 1683984 orphans, 108428 too large [>5000 bp], 109718350 duplicates)
Reads: 346797420 total, 1022765 skipped (flags/unmapped)
Fragments: 173710387 total (171476357 tlen-paired, 95536 hash-paired, 1573 singletons, 178613 discordant, 1958308 orphans, 156881 too large [>5000 bp], 112973528 duplicates)
Reads: 368523010 total, 1207129 skipped (flags/unmapped)
Fragments: 184740711 total (181469678 tlen-paired, 107002 hash-paired, 1983 singletons, 491760 discordant, 2670288 orphans, 253365 too large [>5000 bp], 119796681 duplicates)