Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/169778de3fd9e48099f14a505fc80f/.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/e3/169778de3fd9e48099f14a505fc80f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BL7I-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BL7I-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BL7I-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BL7I-N1-BDNA-1_B23H2GYLT3_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: 84709283 total, 72726 skipped (flags/unmapped)
Fragments: 42508817 total (42088500 tlen-paired, 14245 hash-paired, 7172 singletons, 8263 discordant, 390637 orphans, 8366 too large [>5000 bp], 9192011 duplicates)
Reads: 92426931 total, 65129 skipped (flags/unmapped)
Fragments: 46398932 total (45922500 tlen-paired, 15207 hash-paired, 7447 singletons, 5895 discordant, 447883 orphans, 9634 too large [>5000 bp], 10011964 duplicates)
Reads: 93026820 total, 67180 skipped (flags/unmapped)
Fragments: 46695356 total (46209077 tlen-paired, 15391 hash-paired, 7665 singletons, 8060 discordant, 455163 orphans, 15878 too large [>5000 bp], 10020427 duplicates)
Reads: 95513663 total, 109255 skipped (flags/unmapped)
Fragments: 48174053 total (46716148 tlen-paired, 15164 hash-paired, 7794 singletons, 282131 discordant, 1152816 orphans, 108456 too large [>5000 bp], 10255423 duplicates)