Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_JZ-N1-BDNA-1_B23MHTGLT4_1/1047_JZ-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/1047_JZ-N1-BDNA-1_B23MHTGLT4_1/1047_JZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/7eb7e9186755865b4d5c9e50af88b6/.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/ff/7eb7e9186755865b4d5c9e50af88b6/.command.run
==> 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: 1047_JZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1047_JZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JZ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JZ-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: 106091858 total, 61577 skipped (flags/unmapped)
Fragments: 53296602 total (52693234 tlen-paired, 3741 hash-paired, 676 singletons, 12746 discordant, 586205 orphans, 11979 too large [>5000 bp], 17378782 duplicates)
Reads: 104300127 total, 67613 skipped (flags/unmapped)
Fragments: 52400115 total (51761145 tlen-paired, 5861 hash-paired, 538 singletons, 15811 discordant, 616760 orphans, 24791 too large [>5000 bp], 17538333 duplicates)
Reads: 98608790 total, 74348 skipped (flags/unmapped)
Fragments: 49535823 total (48951330 tlen-paired, 4222 hash-paired, 619 singletons, 17831 discordant, 561821 orphans, 12618 too large [>5000 bp], 16449037 duplicates)
Reads: 116545406 total, 114002 skipped (flags/unmapped)
Fragments: 58802966 total (56945086 tlen-paired, 4533 hash-paired, 618 singletons, 372189 discordant, 1480540 orphans, 153315 too large [>5000 bp], 19607831 duplicates)