Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_I5-N1-BDNA-1_B23MHTGLT4_1/1029_I5-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/394edfd230f8735b214cd391a1af73/.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/e1/394edfd230f8735b214cd391a1af73/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_I5-N1-BDNA-1_B23MHTGLT4_1/1029_I5-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> 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_I5-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I5-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I5-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I5-N1-BDNA-1_B23MHTGLT4_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: 68632372 total, 50679 skipped (flags/unmapped)
Fragments: 34507130 total (34041325 tlen-paired, 2943 hash-paired, 331 singletons, 11145 discordant, 451386 orphans, 9575 too large [>5000 bp], 10890546 duplicates)
Reads: 72979715 total, 42418 skipped (flags/unmapped)
Fragments: 36698465 total (36213637 tlen-paired, 2141 hash-paired, 496 singletons, 7482 discordant, 474709 orphans, 7786 too large [>5000 bp], 11277000 duplicates)
Reads: 79597536 total, 48115 skipped (flags/unmapped)
Fragments: 40020351 total (39471948 tlen-paired, 2877 hash-paired, 342 singletons, 11413 discordant, 533771 orphans, 21416 too large [>5000 bp], 12640398 duplicates)
Reads: 80765323 total, 78757 skipped (flags/unmapped)
Fragments: 40851673 total (39260311 tlen-paired, 3327 hash-paired, 380 singletons, 312057 discordant, 1275598 orphans, 129599 too large [>5000 bp], 12838389 duplicates)