Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6IJ-N1-BDNA-1_B23L5TMLT4_1/1136_6IJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6IJ-N1-BDNA-1_B23L5TMLT4_1/1136_6IJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/93e660336b71765fc582e688830bce/.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/3c/93e660336b71765fc582e688830bce/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6IJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6IJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6IJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6IJ-N1-BDNA-1_B23L5TMLT4_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: 86521425 total, 62463 skipped (flags/unmapped)
Fragments: 43394545 total (43019263 tlen-paired, 4137 hash-paired, 487 singletons, 15925 discordant, 354733 orphans, 12546 too large [>5000 bp], 16097285 duplicates)
Reads: 90969525 total, 57399 skipped (flags/unmapped)
Fragments: 45636488 total (45208598 tlen-paired, 4519 hash-paired, 466 singletons, 14065 discordant, 408840 orphans, 24228 too large [>5000 bp], 16967907 duplicates)
Reads: 91893914 total, 50025 skipped (flags/unmapped)
Fragments: 46096104 total (45713225 tlen-paired, 2875 hash-paired, 561 singletons, 11021 discordant, 368422 orphans, 10332 too large [>5000 bp], 16771157 duplicates)
Reads: 100792570 total, 96732 skipped (flags/unmapped)
Fragments: 50694511 total (49606233 tlen-paired, 5119 hash-paired, 505 singletons, 213269 discordant, 869385 orphans, 88353 too large [>5000 bp], 18833577 duplicates)