Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_5FF-N1-BDNA-1_A23MHW3LT4_1/1029_5FF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/6e35dadc97a81b6727c51451080d56/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_5FF-N1-BDNA-1_A23MHW3LT4_1/1029_5FF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  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/71/6e35dadc97a81b6727c51451080d56/.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: 1029_5FF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5FF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5FF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5FF-N1-BDNA-1_A23MHW3LT4_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: 70407829 total, 61461 skipped (flags/unmapped)
Fragments: 35334475 total (34979587 tlen-paired, 3903 hash-paired, 415 singletons, 9093 discordant, 341477 orphans, 9655 too large [>5000 bp], 11946658 duplicates)
Reads: 74665392 total, 52529 skipped (flags/unmapped)
Fragments: 37486331 total (37098203 tlen-paired, 2580 hash-paired, 603 singletons, 6777 discordant, 378168 orphans, 9486 too large [>5000 bp], 12367784 duplicates)
Reads: 81540500 total, 56050 skipped (flags/unmapped)
Fragments: 40934148 total (40498015 tlen-paired, 6505 hash-paired, 475 singletons, 9250 discordant, 419903 orphans, 18266 too large [>5000 bp], 13790657 duplicates)
Reads: 82605767 total, 99821 skipped (flags/unmapped)
Fragments: 41639872 total (40424392 tlen-paired, 3458 hash-paired, 484 singletons, 240876 discordant, 970662 orphans, 98674 too large [>5000 bp], 13929620 duplicates)