Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BOYY-N1-BDNA-1_B23L5TMLT4_1/1029_BOYY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/bc2a45eb5778709c99fd5c962b69c8/.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/1b/bc2a45eb5778709c99fd5c962b69c8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BOYY-N1-BDNA-1_B23L5TMLT4_1/1029_BOYY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BOYY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BOYY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BOYY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOYY-N1-BDNA-1_B23L5TMLT4_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: 91341623 total, 66933 skipped (flags/unmapped)
Fragments: 45848190 total (45381974 tlen-paired, 4620 hash-paired, 479 singletons, 14986 discordant, 446131 orphans, 12460 too large [>5000 bp], 16980691 duplicates)
Reads: 96038924 total, 56742 skipped (flags/unmapped)
Fragments: 48214475 total (47731143 tlen-paired, 3253 hash-paired, 558 singletons, 10333 discordant, 469188 orphans, 11489 too large [>5000 bp], 17502722 duplicates)
Reads: 96589757 total, 60465 skipped (flags/unmapped)
Fragments: 48487420 total (47960382 tlen-paired, 5479 hash-paired, 461 singletons, 12897 discordant, 508201 orphans, 31557 too large [>5000 bp], 17971917 duplicates)
Reads: 105732952 total, 103043 skipped (flags/unmapped)
Fragments: 53280312 total (51811742 tlen-paired, 2937 hash-paired, 536 singletons, 290758 discordant, 1174339 orphans, 122080 too large [>5000 bp], 19647606 duplicates)