Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0MK-N1-BDNA-1_A23MHW3LT4_1/1136_0MK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/75194a82c98d4ee07596c6760a8a83/.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/d8/75194a82c98d4ee07596c6760a8a83/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0MK-N1-BDNA-1_A23MHW3LT4_1/1136_0MK-N1-BDNA-1_A23MHW3LT4_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: 1136_0MK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0MK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0MK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0MK-N1-BDNA-1_A23MHW3LT4_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: 90784110 total, 70621 skipped (flags/unmapped)
Fragments: 45592037 total (45073193 tlen-paired, 4107 hash-paired, 628 singletons, 19416 discordant, 494693 orphans, 12368 too large [>5000 bp], 15926567 duplicates)
Reads: 104488908 total, 70698 skipped (flags/unmapped)
Fragments: 52475566 total (51853718 tlen-paired, 5476 hash-paired, 533 singletons, 19396 discordant, 596443 orphans, 32027 too large [>5000 bp], 18462056 duplicates)
Reads: 105456136 total, 112235 skipped (flags/unmapped)
Fragments: 53186231 total (51588090 tlen-paired, 4423 hash-paired, 605 singletons, 308165 discordant, 1284948 orphans, 128496 too large [>5000 bp], 18626705 duplicates)
Reads: 95673861 total, 61432 skipped (flags/unmapped)
Fragments: 48047492 total (47522996 tlen-paired, 3243 hash-paired, 611 singletons, 12604 discordant, 508038 orphans, 13047 too large [>5000 bp], 16528610 duplicates)