Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_67D-N1-BDNA-1_B23KGCJLT4_1/1136_67D-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_67D-N1-BDNA-1_B23KGCJLT4_1/1136_67D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/211d0e126fe2bbe9a05bacd0607397/.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/77/211d0e126fe2bbe9a05bacd0607397/.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: 1136_67D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67D-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: 108971610 total, 85952 skipped (flags/unmapped)
Fragments: 54601158 total (54227298 tlen-paired, 4734 hash-paired, 532 singletons, 24740 discordant, 343854 orphans, 13864 too large [>5000 bp], 21612776 duplicates)
Reads: 116463868 total, 77300 skipped (flags/unmapped)
Fragments: 58357982 total (57939623 tlen-paired, 6199 hash-paired, 528 singletons, 21018 discordant, 390614 orphans, 30873 too large [>5000 bp], 23258768 duplicates)
Reads: 118042139 total, 72376 skipped (flags/unmapped)
Fragments: 59140375 total (58775406 tlen-paired, 3665 hash-paired, 659 singletons, 17881 discordant, 342764 orphans, 16218 too large [>5000 bp], 23026215 duplicates)
Reads: 128167044 total, 111463 skipped (flags/unmapped)
Fragments: 64302362 total (63459775 tlen-paired, 4329 hash-paired, 528 singletons, 156181 discordant, 681549 orphans, 66467 too large [>5000 bp], 25701891 duplicates)