Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_HWM-N1-BDNA-1_B23L5TMLT4_1/1029_HWM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/275b78395d7d7bac753f01a78a5121/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_HWM-N1-BDNA-1_B23L5TMLT4_1/1029_HWM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  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/3b/275b78395d7d7bac753f01a78a5121/.command.run
==> 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_HWM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_HWM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HWM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HWM-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: 116931006 total, 84402 skipped (flags/unmapped)
Fragments: 58647050 total (58139537 tlen-paired, 5153 hash-paired, 717 singletons, 22392 discordant, 479251 orphans, 16236 too large [>5000 bp], 20940768 duplicates)
Reads: 122967182 total, 74675 skipped (flags/unmapped)
Fragments: 61683208 total (61124521 tlen-paired, 6240 hash-paired, 599 singletons, 19204 discordant, 532644 orphans, 29667 too large [>5000 bp], 22209306 duplicates)
Reads: 125719225 total, 69626 skipped (flags/unmapped)
Fragments: 63058109 total (62541589 tlen-paired, 5182 hash-paired, 758 singletons, 15939 discordant, 494641 orphans, 14390 too large [>5000 bp], 22203357 duplicates)
Reads: 135517026 total, 124991 skipped (flags/unmapped)
Fragments: 68152988 total (66725287 tlen-paired, 4293 hash-paired, 691 singletons, 275897 discordant, 1146820 orphans, 116785 too large [>5000 bp], 24561119 duplicates)