Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_pO-N1-BDNA-1_B23L5TMLT4_1/659_pO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_pO-N1-BDNA-1_B23L5TMLT4_1/659_pO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/7a7525a4cfce3609c3b2ed954b58d4/.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/1c/7a7525a4cfce3609c3b2ed954b58d4/.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: 659_pO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_pO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_pO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_pO-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 82458775 total, 61724 skipped (flags/unmapped)
Fragments: 41347166 total (41006395 tlen-paired, 4486 hash-paired, 424 singletons, 14912 discordant, 320949 orphans, 12046 too large [>5000 bp], 14417468 duplicates)
Reads: 88833640 total, 51529 skipped (flags/unmapped)
Fragments: 44546730 total (44199137 tlen-paired, 5043 hash-paired, 446 singletons, 9865 discordant, 332239 orphans, 10668 too large [>5000 bp], 15336083 duplicates)
Reads: 96717622 total, 96839 skipped (flags/unmapped)
Fragments: 48629771 total (47642144 tlen-paired, 3769 hash-paired, 414 singletons, 188217 discordant, 795227 orphans, 78441 too large [>5000 bp], 17063151 duplicates)
Reads: 96085195 total, 59135 skipped (flags/unmapped)
Fragments: 48181274 total (47783116 tlen-paired, 6816 hash-paired, 443 singletons, 14904 discordant, 375995 orphans, 19975 too large [>5000 bp], 16913111 duplicates)