Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_ZEN-N1-BDNA-1_B2377KTLT3_2/869_ZEN-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/6648e89453c0df80dba56e1c8db506/.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/3a/6648e89453c0df80dba56e1c8db506/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_ZEN-N1-BDNA-1_B2377KTLT3_2/869_ZEN-N1-BDNA-1_B2377KTLT3_2.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: 869_ZEN-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_2.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: 67675867 total, 53895 skipped (flags/unmapped)
Fragments: 33951142 total (33611406 tlen-paired, 30772 hash-paired, 4852 singletons, 6240 discordant, 297872 orphans, 11206 too large [>5000 bp], 6324769 duplicates)
Reads: 67458412 total, 66776 skipped (flags/unmapped)
Fragments: 33831297 total (33510552 tlen-paired, 29411 hash-paired, 4909 singletons, 6684 discordant, 279741 orphans, 6846 too large [>5000 bp], 6324192 duplicates)
Reads: 74870075 total, 53989 skipped (flags/unmapped)
Fragments: 37562553 total (37204213 tlen-paired, 28772 hash-paired, 5265 singletons, 4948 discordant, 319355 orphans, 7800 too large [>5000 bp], 7005011 duplicates)
Reads: 75504541 total, 97307 skipped (flags/unmapped)
Fragments: 38019580 total (37006976 tlen-paired, 29079 hash-paired, 5238 singletons, 193587 discordant, 784700 orphans, 79006 too large [>5000 bp], 7039549 duplicates)