Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BOXV-N1-BDNA-1_A23MHW3LT4_1/1029_BOXV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/c750f7f3f27e84802f3e0a2789e641/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BOXV-N1-BDNA-1_A23MHW3LT4_1/1029_BOXV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  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/53/c750f7f3f27e84802f3e0a2789e641/.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: 1029_BOXV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOXV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOXV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOXV-N1-BDNA-1_A23MHW3LT4_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: 115695190 total, 99539 skipped (flags/unmapped)
Fragments: 58102951 total (57423655 tlen-paired, 7151 hash-paired, 686 singletons, 26074 discordant, 645385 orphans, 17910 too large [>5000 bp], 20512013 duplicates)
Reads: 133427540 total, 83174 skipped (flags/unmapped)
Fragments: 67015307 total (66239644 tlen-paired, 7291 hash-paired, 581 singletons, 25990 discordant, 741801 orphans, 28067 too large [>5000 bp], 23802386 duplicates)
Reads: 122380445 total, 77213 skipped (flags/unmapped)
Fragments: 61462600 total (60786165 tlen-paired, 4342 hash-paired, 759 singletons, 17659 discordant, 653675 orphans, 16233 too large [>5000 bp], 21373574 duplicates)
Reads: 135788962 total, 130927 skipped (flags/unmapped)
Fragments: 68485526 total (66446762 tlen-paired, 3725 hash-paired, 600 singletons, 392582 discordant, 1641857 orphans, 164720 too large [>5000 bp], 24273483 duplicates)