Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_2/869_G71-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/cede6bddf2764c04a1744cc4b64116/.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/ef/cede6bddf2764c04a1744cc4b64116/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_2/869_G71-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] [W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.baiThe index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G71-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: 140363772 total, 101026 skipped (flags/unmapped)
Fragments: 70392005 total (69738968 tlen-paired, 69405 hash-paired, 9576 singletons, 13142 discordant, 560914 orphans, 24613 too large [>5000 bp], 20037313 duplicates)
Reads: 128079398 total, 113827 skipped (flags/unmapped)
Fragments: 64213965 total (63648621 tlen-paired, 64268 hash-paired, 8793 singletons, 12463 discordant, 479820 orphans, 13127 too large [>5000 bp], 18341115 duplicates)
Reads: 138676407 total, 100513 skipped (flags/unmapped)
Fragments: 69545640 total (68922146 tlen-paired, 68975 hash-paired, 9416 singletons, 8855 discordant, 536248 orphans, 15139 too large [>5000 bp], 19871643 duplicates)
Reads: 143719200 total, 178891 skipped (flags/unmapped)
Fragments: 72321347 total (70556533 tlen-paired, 72284 hash-paired, 9889 singletons, 326921 discordant, 1355720 orphans, 131612 too large [>5000 bp], 20518324 duplicates)