Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BEFS-N1-BDNA-1_B23KFG5LT4_1/1029_BEFS-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/921244b93fd8e7556be6f0a45fdf1a/.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/8f/921244b93fd8e7556be6f0a45fdf1a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BEFS-N1-BDNA-1_B23KFG5LT4_1/1029_BEFS-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BEFS-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BEFS-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BEFS-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BEFS-N1-BDNA-1_B23KFG5LT4_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: 84197519 total, 65153 skipped (flags/unmapped)
Fragments: 42218960 total (41859043 tlen-paired, 3809 hash-paired, 495 singletons, 17544 discordant, 338069 orphans, 16505 too large [>5000 bp], 18089682 duplicates)
Reads: 88868044 total, 54191 skipped (flags/unmapped)
Fragments: 44566609 total (44207929 tlen-paired, 3168 hash-paired, 510 singletons, 12263 discordant, 342739 orphans, 11942 too large [>5000 bp], 18648075 duplicates)
Reads: 98569279 total, 56248 skipped (flags/unmapped)
Fragments: 49435609 total (49016349 tlen-paired, 3293 hash-paired, 336 singletons, 18784 discordant, 396847 orphans, 19498 too large [>5000 bp], 21184589 duplicates)
Reads: 99503028 total, 86840 skipped (flags/unmapped)
Fragments: 50029640 total (49037689 tlen-paired, 3646 hash-paired, 369 singletons, 189395 discordant, 798541 orphans, 77909 too large [>5000 bp], 21450902 duplicates)