Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_20J-N1-BDNA-1_A23MHW3LT4_1/1136_20J-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_20J-N1-BDNA-1_A23MHW3LT4_1/1136_20J-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/706a5375d3f75ce6f6c471a3fb465b/.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/2c/706a5375d3f75ce6f6c471a3fb465b/.command.run
==> 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_20J-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20J-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20J-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20J-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: 98302714 total, 80562 skipped (flags/unmapped)
Fragments: 49424873 total (48739940 tlen-paired, 4073 hash-paired, 472 singletons, 22396 discordant, 657992 orphans, 15435 too large [>5000 bp], 19103157 duplicates)
Reads: 105181168 total, 67478 skipped (flags/unmapped)
Fragments: 52885076 total (52180287 tlen-paired, 3165 hash-paired, 679 singletons, 15858 discordant, 685087 orphans, 14652 too large [>5000 bp], 20048080 duplicates)
Reads: 114331787 total, 74876 skipped (flags/unmapped)
Fragments: 57495906 total (56674945 tlen-paired, 4706 hash-paired, 473 singletons, 23342 discordant, 792440 orphans, 29006 too large [>5000 bp], 22290691 duplicates)
Reads: 116903326 total, 137119 skipped (flags/unmapped)
Fragments: 59081993 total (56888911 tlen-paired, 5327 hash-paired, 545 singletons, 430426 discordant, 1756784 orphans, 179775 too large [>5000 bp], 22739218 duplicates)