Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_13P-N1-BDNA-1_A23MHW3LT4_1/1136_13P-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/e38b2372f6ca2e8a592facb4b87808/.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/68/e38b2372f6ca2e8a592facb4b87808/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_13P-N1-BDNA-1_A23MHW3LT4_1/1136_13P-N1-BDNA-1_A23MHW3LT4_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: 1136_13P-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_13P-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_13P-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_13P-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: 75960103 total, 49763 skipped (flags/unmapped)
Fragments: 38163164 total (37711009 tlen-paired, 3915 hash-paired, 466 singletons, 9336 discordant, 438438 orphans, 11458 too large [>5000 bp], 13112826 duplicates)
Reads: 72395618 total, 56278 skipped (flags/unmapped)
Fragments: 36372024 total (35926242 tlen-paired, 2740 hash-paired, 465 singletons, 13862 discordant, 428715 orphans, 12236 too large [>5000 bp], 12812212 duplicates)
Reads: 84174467 total, 87926 skipped (flags/unmapped)
Fragments: 42498586 total (41070096 tlen-paired, 2754 hash-paired, 435 singletons, 278803 discordant, 1146498 orphans, 118151 too large [>5000 bp], 14861080 duplicates)
Reads: 82960925 total, 52850 skipped (flags/unmapped)
Fragments: 41687167 total (41164904 tlen-paired, 3727 hash-paired, 422 singletons, 13681 discordant, 504433 orphans, 19298 too large [>5000 bp], 14647350 duplicates)