Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_SPC-N1-BDNA-1_B2377KTLT3_2/869_SPC-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/9135c197914be051d8be605ecf5b62/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_SPC-N1-BDNA-1_B2377KTLT3_2/869_SPC-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  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/00/9135c197914be051d8be605ecf5b62/.command.run
==> 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: 869_SPC-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_2.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: 70748428 total, 64068 skipped (flags/unmapped)
Fragments: 35505028 total (35134011 tlen-paired, 18656 hash-paired, 4422 singletons, 6953 discordant, 340986 orphans, 9856 too large [>5000 bp], 7054083 duplicates)
Reads: 77489341 total, 52570 skipped (flags/unmapped)
Fragments: 38906236 total (38490672 tlen-paired, 19062 hash-paired, 4771 singletons, 4949 discordant, 386782 orphans, 7926 too large [>5000 bp], 7767664 duplicates)
Reads: 78069366 total, 54917 skipped (flags/unmapped)
Fragments: 39192863 total (38766923 tlen-paired, 19832 hash-paired, 4685 singletons, 7201 discordant, 394222 orphans, 13815 too large [>5000 bp], 7772364 duplicates)
Reads: 79994130 total, 96554 skipped (flags/unmapped)
Fragments: 40355921 total (39080251 tlen-paired, 21116 hash-paired, 4892 singletons, 246132 discordant, 1003530 orphans, 97078 too large [>5000 bp], 7920815 duplicates)