Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/457344ca97f2dac3cb5352f141ebc0/.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/ca/457344ca97f2dac3cb5352f141ebc0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_WTT-N1-BDNA-1_B23H2GYLT3_1/1029_WTT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_WTT-N1-BDNA-1_B23H2GYLT3_1/1029_WTT-N1-BDNA-1_B23H2GYLT3_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_WTT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_WTT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_WTT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_WTT-N1-BDNA-1_B23H2GYLT3_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: 79661231 total, 72346 skipped (flags/unmapped)
Fragments: 39972303 total (39574963 tlen-paired, 15326 hash-paired, 5966 singletons, 8541 discordant, 367507 orphans, 8876 too large [>5000 bp], 8590244 duplicates)
Reads: 87184858 total, 59217 skipped (flags/unmapped)
Fragments: 43766767 total (43320349 tlen-paired, 15313 hash-paired, 6420 singletons, 5900 discordant, 418785 orphans, 8656 too large [>5000 bp], 9390973 duplicates)
Reads: 87447416 total, 67460 skipped (flags/unmapped)
Fragments: 43892783 total (43431694 tlen-paired, 19304 hash-paired, 6451 singletons, 8565 discordant, 426769 orphans, 13805 too large [>5000 bp], 9383017 duplicates)
Reads: 89679793 total, 110052 skipped (flags/unmapped)
Fragments: 45221387 total (43861603 tlen-paired, 16862 hash-paired, 6712 singletons, 262771 discordant, 1073439 orphans, 103559 too large [>5000 bp], 9576913 duplicates)