Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BJUI-N1-BDNA-1_B23MHTGLT4_1/1029_BJUI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/1ed80be0144ce97aa60f7319ee4e7d/.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/c6/1ed80be0144ce97aa60f7319ee4e7d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BJUI-N1-BDNA-1_B23MHTGLT4_1/1029_BJUI-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_BJUI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJUI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJUI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJUI-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: 68492039 total, 38418 skipped (flags/unmapped)
Fragments: 34394539 total (34034549 tlen-paired, 2222 hash-paired, 426 singletons, 7455 discordant, 349887 orphans, 7428 too large [>5000 bp], 10096972 duplicates)
Reads: 65435301 total, 48561 skipped (flags/unmapped)
Fragments: 32854641 total (32500114 tlen-paired, 2243 hash-paired, 392 singletons, 10658 discordant, 341234 orphans, 9542 too large [>5000 bp], 9830567 duplicates)
Reads: 75356901 total, 44024 skipped (flags/unmapped)
Fragments: 37840019 total (37432734 tlen-paired, 2704 hash-paired, 376 singletons, 10664 discordant, 393541 orphans, 13378 too large [>5000 bp], 11382365 duplicates)
Reads: 75963183 total, 73057 skipped (flags/unmapped)
Fragments: 38312532 total (37163085 tlen-paired, 1561 hash-paired, 452 singletons, 224104 discordant, 923330 orphans, 94422 too large [>5000 bp], 11506173 duplicates)