Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_G60-N1-BDNA-1_B23KFG5LT4_1/1029_G60-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/1029_G60-N1-BDNA-1_B23KFG5LT4_1/1029_G60-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/801b48f017060c820ee0a29dfc0692/.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/29/801b48f017060c820ee0a29dfc0692/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_G60-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_G60-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G60-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G60-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: 69775102 total, 53215 skipped (flags/unmapped)
Fragments: 34990360 total (34687414 tlen-paired, 2849 hash-paired, 366 singletons, 18690 discordant, 281041 orphans, 11287 too large [>5000 bp], 14351444 duplicates)
Reads: 82335763 total, 75928 skipped (flags/unmapped)
Fragments: 41376735 total (40628235 tlen-paired, 1909 hash-paired, 316 singletons, 139834 discordant, 606441 orphans, 56561 too large [>5000 bp], 16967553 duplicates)
Reads: 73523981 total, 44822 skipped (flags/unmapped)
Fragments: 36868325 total (36573438 tlen-paired, 3203 hash-paired, 438 singletons, 12251 discordant, 278995 orphans, 10971 too large [>5000 bp], 14746138 duplicates)
Reads: 81549993 total, 49895 skipped (flags/unmapped)
Fragments: 40897017 total (40548093 tlen-paired, 4464 hash-paired, 292 singletons, 17784 discordant, 326384 orphans, 16370 too large [>5000 bp], 16755769 duplicates)