Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_3D3-N1-BDNA-1_B23KGCJLT4_1/1136_3D3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/4558b557e92005fe85fa7999174113/.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/0a/4558b557e92005fe85fa7999174113/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_3D3-N1-BDNA-1_B23KGCJLT4_1/1136_3D3-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_3D3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3D3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3D3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3D3-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: 61913539 total, 44147 skipped (flags/unmapped)
Fragments: 31015756 total (30826426 tlen-paired, 2854 hash-paired, 269 singletons, 11050 discordant, 175157 orphans, 6653 too large [>5000 bp], 10774650 duplicates)
Reads: 66807475 total, 36179 skipped (flags/unmapped)
Fragments: 33466798 total (33278084 tlen-paired, 2746 hash-paired, 301 singletons, 8028 discordant, 177639 orphans, 7820 too large [>5000 bp], 11412434 duplicates)
Reads: 66385864 total, 39393 skipped (flags/unmapped)
Fragments: 33258758 total (33037135 tlen-paired, 4462 hash-paired, 238 singletons, 9720 discordant, 207203 orphans, 18198 too large [>5000 bp], 11604944 duplicates)
Reads: 73013208 total, 61506 skipped (flags/unmapped)
Fragments: 36623985 total (36156806 tlen-paired, 2728 hash-paired, 277 singletons, 88677 discordant, 375497 orphans, 39753 too large [>5000 bp], 12807048 duplicates)