Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/c2fbdcdbe3f2d3c5dd1a20878c4f85/.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/19/c2fbdcdbe3f2d3c5dd1a20878c4f85/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_367-N1-BDNA-1_B23KFG5LT4_1/1136_367-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_367-N1-BDNA-1_B23KFG5LT4_1/1136_367-N1-BDNA-1_B23KFG5LT4_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_367-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_367-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_367-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_367-N1-BDNA-1_B23KFG5LT4_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: 81368530 total, 59684 skipped (flags/unmapped)
Fragments: 40771945 total (40495449 tlen-paired, 3053 hash-paired, 350 singletons, 16805 discordant, 256288 orphans, 10797 too large [>5000 bp], 15540948 duplicates)
Reads: 86732647 total, 56627 skipped (flags/unmapped)
Fragments: 43461465 total (43139570 tlen-paired, 4115 hash-paired, 338 singletons, 14574 discordant, 302868 orphans, 28148 too large [>5000 bp], 16615663 duplicates)
Reads: 87550593 total, 49494 skipped (flags/unmapped)
Fragments: 43871093 total (43595458 tlen-paired, 3085 hash-paired, 447 singletons, 11907 discordant, 260196 orphans, 9778 too large [>5000 bp], 16294996 duplicates)
Reads: 95450851 total, 90128 skipped (flags/unmapped)
Fragments: 47900243 total (47225680 tlen-paired, 2764 hash-paired, 426 singletons, 125870 discordant, 545503 orphans, 53083 too large [>5000 bp], 18401160 duplicates)