Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BJVE-N1-BDNA-1_A23TY32LT4_1/1241_BJVE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/ee1230434adafb84a5d2491a073617/.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/22/ee1230434adafb84a5d2491a073617/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BJVE-N1-BDNA-1_A23TY32LT4_1/1241_BJVE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> 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: 1241_BJVE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJVE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJVE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJVE-N1-BDNA-1_A23TY32LT4_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: 88503034 total, 65725 skipped (flags/unmapped)
Fragments: 44382120 total (44016143 tlen-paired, 4351 hash-paired, 397 singletons, 13923 discordant, 347306 orphans, 10386 too large [>5000 bp], 17884381 duplicates)
Reads: 95011725 total, 56253 skipped (flags/unmapped)
Fragments: 47652463 total (47271647 tlen-paired, 2842 hash-paired, 460 singletons, 9410 discordant, 368104 orphans, 9555 too large [>5000 bp], 19021053 duplicates)
Reads: 104597640 total, 60352 skipped (flags/unmapped)
Fragments: 52462971 total (52015523 tlen-paired, 5068 hash-paired, 355 singletons, 14312 discordant, 427713 orphans, 19707 too large [>5000 bp], 21273279 duplicates)
Reads: 105940487 total, 107726 skipped (flags/unmapped)
Fragments: 53281696 total (52142219 tlen-paired, 4118 hash-paired, 451 singletons, 223606 discordant, 911302 orphans, 90561 too large [>5000 bp], 21527809 duplicates)