Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_FQ3-N1-BDNA-1_A23TNVNLT4_1/1241_FQ3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/a170885ce7eeaec1336f41a14bb3b1/.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/f5/a170885ce7eeaec1336f41a14bb3b1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_FQ3-N1-BDNA-1_A23TNVNLT4_1/1241_FQ3-N1-BDNA-1_A23TNVNLT4_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_FQ3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FQ3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FQ3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FQ3-N1-BDNA-1_A23TNVNLT4_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: 78101948 total, 58944 skipped (flags/unmapped)
Fragments: 39130159 total (38871787 tlen-paired, 5409 hash-paired, 335 singletons, 14309 discordant, 238319 orphans, 10670 too large [>5000 bp], 13945161 duplicates)
Reads: 83343858 total, 50619 skipped (flags/unmapped)
Fragments: 41760618 total (41479489 tlen-paired, 5027 hash-paired, 347 singletons, 12607 discordant, 263148 orphans, 17749 too large [>5000 bp], 14989380 duplicates)
Reads: 84424524 total, 49580 skipped (flags/unmapped)
Fragments: 42299809 total (42041233 tlen-paired, 5011 hash-paired, 458 singletons, 10425 discordant, 242682 orphans, 9233 too large [>5000 bp], 14831357 duplicates)
Reads: 91843976 total, 91569 skipped (flags/unmapped)
Fragments: 46085433 total (45433591 tlen-paired, 5375 hash-paired, 432 singletons, 123966 discordant, 522069 orphans, 52021 too large [>5000 bp], 16576514 duplicates)