Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_6YX-N1-BDNA-1_B23KGCJLT4_1/1136_6YX-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/e25b4a8bb9e5565ba6a65195ad4879/.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/5f/e25b4a8bb9e5565ba6a65195ad4879/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_6YX-N1-BDNA-1_B23KGCJLT4_1/1136_6YX-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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_6YX-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6YX-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6YX-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6YX-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: 77756946 total, 57177 skipped (flags/unmapped)
Fragments: 38952424 total (38707390 tlen-paired, 3247 hash-paired, 334 singletons, 13998 discordant, 227455 orphans, 11355 too large [>5000 bp], 14044129 duplicates)
Reads: 82345455 total, 44244 skipped (flags/unmapped)
Fragments: 41255024 total (41014508 tlen-paired, 2570 hash-paired, 408 singletons, 9533 discordant, 228005 orphans, 9788 too large [>5000 bp], 14629477 duplicates)
Reads: 90499981 total, 80885 skipped (flags/unmapped)
Fragments: 45406611 total (44795037 tlen-paired, 2299 hash-paired, 376 singletons, 111891 discordant, 497008 orphans, 51629 too large [>5000 bp], 16484375 duplicates)
Reads: 90909399 total, 52688 skipped (flags/unmapped)
Fragments: 45545996 total (45247689 tlen-paired, 3532 hash-paired, 356 singletons, 14552 discordant, 279867 orphans, 22471 too large [>5000 bp], 16487438 duplicates)