Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_OSZ-N1-BDNA-1_B23MHTGLT4_1/1029_OSZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_OSZ-N1-BDNA-1_B23MHTGLT4_1/1029_OSZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/03f3f998f99ac1beb1485f3d3c33a3/.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/97/03f3f998f99ac1beb1485f3d3c33a3/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_OSZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_OSZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OSZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OSZ-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: 74405924 total, 52082 skipped (flags/unmapped)
Fragments: 37324759 total (36998533 tlen-paired, 2974 hash-paired, 378 singletons, 13226 discordant, 309648 orphans, 7175 too large [>5000 bp], 10973993 duplicates)
Reads: 86742293 total, 76945 skipped (flags/unmapped)
Fragments: 43640278 total (42685902 tlen-paired, 3777 hash-paired, 461 singletons, 181813 discordant, 768325 orphans, 76789 too large [>5000 bp], 12910799 duplicates)
Reads: 78971172 total, 45648 skipped (flags/unmapped)
Fragments: 39611129 total (39283785 tlen-paired, 2875 hash-paired, 416 singletons, 9405 discordant, 314648 orphans, 9165 too large [>5000 bp], 11390559 duplicates)
Reads: 85835326 total, 50344 skipped (flags/unmapped)
Fragments: 43054578 total (42665648 tlen-paired, 4995 hash-paired, 392 singletons, 13555 discordant, 369988 orphans, 23103 too large [>5000 bp], 12723545 duplicates)