Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_7Y1-N1-BDNA-1_2375WFLT3_s16/1029_7Y1-N1-BDNA-1_2375WFLT3_s16.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/b508b0f125c0606ba7b34c59aa9d57/.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/48/b508b0f125c0606ba7b34c59aa9d57/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_7Y1-N1-BDNA-1_2375WFLT3_s16/1029_7Y1-N1-BDNA-1_2375WFLT3_s16.recalibrated.bam.bai
==> 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_7Y1-N1-BDNA-1_2375WFLT3_s16.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-N1-BDNA-1_2375WFLT3_s16.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-N1-BDNA-1_2375WFLT3_s16.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-N1-BDNA-1_2375WFLT3_s16.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: 68566513 total, 63781 skipped (flags/unmapped)
Fragments: 34483838 total (33989040 tlen-paired, 4006 hash-paired, 1126 singletons, 13762 discordant, 475904 orphans, 6043 too large [>5000 bp], 10193074 duplicates)
Reads: 73857898 total, 57652 skipped (flags/unmapped)
Fragments: 37148562 total (36619749 tlen-paired, 3162 hash-paired, 1203 singletons, 9679 discordant, 514769 orphans, 9547 too large [>5000 bp], 10826580 duplicates)
Reads: 75479259 total, 60773 skipped (flags/unmapped)
Fragments: 37960875 total (37405614 tlen-paired, 4572 hash-paired, 1220 singletons, 13473 discordant, 535996 orphans, 16976 too large [>5000 bp], 11117631 duplicates)
Reads: 77330153 total, 111037 skipped (flags/unmapped)
Fragments: 39139950 total (37507158 tlen-paired, 3824 hash-paired, 1247 singletons, 314850 discordant, 1312871 orphans, 126667 too large [>5000 bp], 11373491 duplicates)