Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_EZD-N1-BDNA-1_B23H3Y2LT3_1/869_EZD-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/0eaec6a63d8eba508ec308c02d43e0/.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/73/0eaec6a63d8eba508ec308c02d43e0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_EZD-N1-BDNA-1_B23H3Y2LT3_1/869_EZD-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
==> 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_EZD-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EZD-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EZD-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EZD-N1-BDNA-1_B23H3Y2LT3_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: 92490924 total, 88370 skipped (flags/unmapped)
Fragments: 46505058 total (45855840 tlen-paired, 13639 hash-paired, 3010 singletons, 10753 discordant, 621816 orphans, 8632 too large [>5000 bp], 10798178 duplicates)
Reads: 92815050 total, 77031 skipped (flags/unmapped)
Fragments: 46679710 total (46007518 tlen-paired, 13839 hash-paired, 3151 singletons, 9164 discordant, 646038 orphans, 13894 too large [>5000 bp], 10802855 duplicates)
Reads: 101450045 total, 77887 skipped (flags/unmapped)
Fragments: 51024006 total (50305072 tlen-paired, 14596 hash-paired, 3377 singletons, 7824 discordant, 693137 orphans, 10330 too large [>5000 bp], 11834873 duplicates)
Reads: 105227724 total, 205177 skipped (flags/unmapped)
Fragments: 53229347 total (50965624 tlen-paired, 15200 hash-paired, 3725 singletons, 449936 discordant, 1794862 orphans, 181220 too large [>5000 bp], 12143283 duplicates)