Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_3YU-N1-BDNA-1_B23L5TMLT4_1/1136_3YU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/d8af42b15abc11dd49f7ec1c226a9b/.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/69/d8af42b15abc11dd49f7ec1c226a9b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_3YU-N1-BDNA-1_B23L5TMLT4_1/1136_3YU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3YU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3YU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3YU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3YU-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: 115101942 total, 71634 skipped (flags/unmapped)
Fragments: 57717416 total (57263080 tlen-paired, 6192 hash-paired, 676 singletons, 15380 discordant, 432088 orphans, 14120 too large [>5000 bp], 22175863 duplicates)
Reads: 107070724 total, 85326 skipped (flags/unmapped)
Fragments: 53686739 total (53236076 tlen-paired, 5673 hash-paired, 730 singletons, 21894 discordant, 422366 orphans, 17508 too large [>5000 bp], 20901394 duplicates)
Reads: 114165380 total, 73785 skipped (flags/unmapped)
Fragments: 57252006 total (56755265 tlen-paired, 6592 hash-paired, 619 singletons, 18770 discordant, 470760 orphans, 29481 too large [>5000 bp], 22428334 duplicates)
Reads: 126026657 total, 129751 skipped (flags/unmapped)
Fragments: 63341503 total (62110848 tlen-paired, 5664 hash-paired, 702 singletons, 238481 discordant, 985808 orphans, 100205 too large [>5000 bp], 24754796 duplicates)