Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_XZ9-N1-BDNA-1_B23L5TMLT4_1/1029_XZ9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/9a931d71afb0e632b09a8b00866aa3/.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/5a/9a931d71afb0e632b09a8b00866aa3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_XZ9-N1-BDNA-1_B23L5TMLT4_1/1029_XZ9-N1-BDNA-1_B23L5TMLT4_1.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: 1029_XZ9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XZ9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XZ9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XZ9-N1-BDNA-1_B23L5TMLT4_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: 105458895 total, 84366 skipped (flags/unmapped)
Fragments: 52933419 total (52384888 tlen-paired, 5537 hash-paired, 590 singletons, 19005 discordant, 523399 orphans, 15840 too large [>5000 bp], 20198692 duplicates)
Reads: 112020511 total, 70389 skipped (flags/unmapped)
Fragments: 56236225 total (55664792 tlen-paired, 5474 hash-paired, 730 singletons, 12959 discordant, 552270 orphans, 15336 too large [>5000 bp], 21144763 duplicates)
Reads: 121935152 total, 75630 skipped (flags/unmapped)
Fragments: 61213622 total (60552236 tlen-paired, 7606 hash-paired, 597 singletons, 18904 discordant, 634279 orphans, 33577 too large [>5000 bp], 23456015 duplicates)
Reads: 122746386 total, 142187 skipped (flags/unmapped)
Fragments: 61859925 total (60126895 tlen-paired, 4440 hash-paired, 647 singletons, 334185 discordant, 1393758 orphans, 139377 too large [>5000 bp], 23580130 duplicates)