Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/3d53668919033df44928734419834e/.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/f0/3d53668919033df44928734419834e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_GD-N1-BDNA-1_B23KGCJLT4_1/1047_GD-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/1047_GD-N1-BDNA-1_B23KGCJLT4_1/1047_GD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_GD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_GD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_GD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_GD-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: 76766174 total, 49821 skipped (flags/unmapped)
Fragments: 38505329 total (38173962 tlen-paired, 2557 hash-paired, 429 singletons, 11047 discordant, 317334 orphans, 11729 too large [>5000 bp], 15748971 duplicates)
Reads: 71296843 total, 56445 skipped (flags/unmapped)
Fragments: 35762251 total (35442587 tlen-paired, 2634 hash-paired, 321 singletons, 15540 discordant, 301169 orphans, 8693 too large [>5000 bp], 14867393 duplicates)
Reads: 76418938 total, 53904 skipped (flags/unmapped)
Fragments: 38336845 total (37967179 tlen-paired, 2277 hash-paired, 345 singletons, 13547 discordant, 353497 orphans, 22593 too large [>5000 bp], 16078687 duplicates)
Reads: 84393073 total, 86390 skipped (flags/unmapped)
Fragments: 42439289 total (41548735 tlen-paired, 2183 hash-paired, 407 singletons, 173630 discordant, 714334 orphans, 71423 too large [>5000 bp], 17809378 duplicates)