Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_0B-N1-BDNA-1_B23H2GYLT3_1/1136_0B-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_0B-N1-BDNA-1_B23H2GYLT3_1/1136_0B-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/0040624db6f29407871c08f3c81322/.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/9b/0040624db6f29407871c08f3c81322/.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_0B-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B-N1-BDNA-1_B23H2GYLT3_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: 56470074 total, 50262 skipped (flags/unmapped)
Fragments: 28345292 total (28050572 tlen-paired, 8905 hash-paired, 4523 singletons, 6055 discordant, 275237 orphans, 4494 too large [>5000 bp], 5585913 duplicates)
Reads: 61946971 total, 42930 skipped (flags/unmapped)
Fragments: 31106548 total (30771442 tlen-paired, 9473 hash-paired, 4788 singletons, 4244 discordant, 316601 orphans, 6167 too large [>5000 bp], 6109709 duplicates)
Reads: 62413678 total, 45729 skipped (flags/unmapped)
Fragments: 31336467 total (30998518 tlen-paired, 9648 hash-paired, 4740 singletons, 5824 discordant, 317737 orphans, 8746 too large [>5000 bp], 6134783 duplicates)
Reads: 63725089 total, 82135 skipped (flags/unmapped)
Fragments: 32153669 total (31128350 tlen-paired, 9107 hash-paired, 4960 singletons, 198592 discordant, 812660 orphans, 76618 too large [>5000 bp], 6213202 duplicates)