Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_7AL-N1-BDNA-1_A23KFG7LT4_1/1136_7AL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_7AL-N1-BDNA-1_A23KFG7LT4_1/1136_7AL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/2662c483330322a31f8750f3d2a025/.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/28/2662c483330322a31f8750f3d2a025/.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_7AL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7AL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7AL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7AL-N1-BDNA-1_A23KFG7LT4_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: 91676782 total, 61425 skipped (flags/unmapped)
Fragments: 45927792 total (45641632 tlen-paired, 4408 hash-paired, 408 singletons, 15123 discordant, 266221 orphans, 13201 too large [>5000 bp], 16808557 duplicates)
Reads: 97005438 total, 48937 skipped (flags/unmapped)
Fragments: 48603522 total (48318048 tlen-paired, 3357 hash-paired, 440 singletons, 10638 discordant, 271039 orphans, 10468 too large [>5000 bp], 17333473 duplicates)
Reads: 96831575 total, 52898 skipped (flags/unmapped)
Fragments: 48522511 total (48190589 tlen-paired, 5305 hash-paired, 359 singletons, 12774 discordant, 313484 orphans, 23749 too large [>5000 bp], 17738015 duplicates)
Reads: 106701928 total, 86498 skipped (flags/unmapped)
Fragments: 53546310 total (52794415 tlen-paired, 4061 hash-paired, 453 singletons, 144918 discordant, 602463 orphans, 62863 too large [>5000 bp], 19645188 duplicates)