Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_BTXK-N1-BDNA-1_A23H3NYLT3_1/1029_BTXK-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/1f19169ece8b476bc66a0f4a0204af/.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/10/1f19169ece8b476bc66a0f4a0204af/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_BTXK-N1-BDNA-1_A23H3NYLT3_1/1029_BTXK-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
==> 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: 1029_BTXK-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BTXK-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BTXK-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BTXK-N1-BDNA-1_A23H3NYLT3_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: 72079724 total, 64535 skipped (flags/unmapped)
Fragments: 36217574 total (35763050 tlen-paired, 11190 hash-paired, 6504 singletons, 7193 discordant, 429637 orphans, 8091 too large [>5000 bp], 5161135 duplicates)
Reads: 77390432 total, 57695 skipped (flags/unmapped)
Fragments: 38900269 total (38380973 tlen-paired, 14180 hash-paired, 6898 singletons, 7359 discordant, 490859 orphans, 14978 too large [>5000 bp], 5512448 duplicates)
Reads: 78511618 total, 55238 skipped (flags/unmapped)
Fragments: 39475806 total (38945989 tlen-paired, 11562 hash-paired, 6765 singletons, 5755 discordant, 505735 orphans, 8634 too large [>5000 bp], 5529970 duplicates)
Reads: 79392551 total, 97098 skipped (flags/unmapped)
Fragments: 40179746 total (38550401 tlen-paired, 11569 hash-paired, 6832 singletons, 319211 discordant, 1291733 orphans, 117263 too large [>5000 bp], 5606633 duplicates)