Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BBAU-N1-BDNA-1_A23MHW3LT4_1/1029_BBAU-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/7e6145e4a5157d06e317654d3c1fb3/.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/aa/7e6145e4a5157d06e317654d3c1fb3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BBAU-N1-BDNA-1_A23MHW3LT4_1/1029_BBAU-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BBAU-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBAU-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BBAU-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBAU-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: 83322415 total, 50590 skipped (flags/unmapped)
Fragments: 41883225 total (41353666 tlen-paired, 3163 hash-paired, 563 singletons, 8855 discordant, 516978 orphans, 11458 too large [>5000 bp], 14538510 duplicates)
Reads: 78185787 total, 56312 skipped (flags/unmapped)
Fragments: 39295691 total (38797626 tlen-paired, 3199 hash-paired, 435 singletons, 11687 discordant, 482744 orphans, 10636 too large [>5000 bp], 14012565 duplicates)
Reads: 90616006 total, 54567 skipped (flags/unmapped)
Fragments: 45548607 total (44960620 tlen-paired, 5745 hash-paired, 414 singletons, 11773 discordant, 570055 orphans, 17347 too large [>5000 bp], 16240352 duplicates)
Reads: 92602944 total, 93851 skipped (flags/unmapped)
Fragments: 46801319 total (45080987 tlen-paired, 3583 hash-paired, 491 singletons, 340334 discordant, 1375924 orphans, 141435 too large [>5000 bp], 16586010 duplicates)