Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_drc-N1-BDNA-1_B23L5TMLT4_1/659_drc-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/286849fa3024679812c2bef43157fb/.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/f2/286849fa3024679812c2bef43157fb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_drc-N1-BDNA-1_B23L5TMLT4_1/659_drc-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> 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: 659_drc-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drc-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drc-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drc-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: 67262154 total, 51511 skipped (flags/unmapped)
Fragments: 33733074 total (33444916 tlen-paired, 3742 hash-paired, 342 singletons, 10435 discordant, 273639 orphans, 9238 too large [>5000 bp], 11586366 duplicates)
Reads: 71280689 total, 41092 skipped (flags/unmapped)
Fragments: 35754018 total (35459911 tlen-paired, 2902 hash-paired, 413 singletons, 7054 discordant, 283738 orphans, 7856 too large [>5000 bp], 12104452 duplicates)
Reads: 78460474 total, 47295 skipped (flags/unmapped)
Fragments: 39356838 total (39015116 tlen-paired, 5353 hash-paired, 344 singletons, 10028 discordant, 325997 orphans, 12922 too large [>5000 bp], 13578729 duplicates)
Reads: 79264739 total, 82345 skipped (flags/unmapped)
Fragments: 39878061 total (38984425 tlen-paired, 3626 hash-paired, 338 singletons, 173234 discordant, 716438 orphans, 71524 too large [>5000 bp], 13700483 duplicates)