Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_C8-N1-BDNA-1_B23L5TMLT4_1/1047_C8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/1330d385b34153f5a55637e7938ea4/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_C8-N1-BDNA-1_B23L5TMLT4_1/1047_C8-N1-BDNA-1_B23L5TMLT4_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/a8/1330d385b34153f5a55637e7938ea4/.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: 1047_C8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_C8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_C8-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: 93774117 total, 72485 skipped (flags/unmapped)
Fragments: 47059554 total (46592182 tlen-paired, 5336 hash-paired, 657 singletons, 18780 discordant, 442599 orphans, 12890 too large [>5000 bp], 17490476 duplicates)
Reads: 98951895 total, 60935 skipped (flags/unmapped)
Fragments: 49660140 total (49187715 tlen-paired, 3613 hash-paired, 639 singletons, 12704 discordant, 455469 orphans, 13394 too large [>5000 bp], 18187573 duplicates)
Reads: 109268825 total, 117504 skipped (flags/unmapped)
Fragments: 55023379 total (53628575 tlen-paired, 5014 hash-paired, 617 singletons, 267627 discordant, 1121546 orphans, 113363 too large [>5000 bp], 20438859 duplicates)
Reads: 108320452 total, 67598 skipped (flags/unmapped)
Fragments: 54363067 total (53822085 tlen-paired, 5054 hash-paired, 614 singletons, 18076 discordant, 517238 orphans, 22286 too large [>5000 bp], 20305855 duplicates)