Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BAMB-N1-BDNA-1_A23KFG7LT4_1/1029_BAMB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BAMB-N1-BDNA-1_A23KFG7LT4_1/1029_BAMB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/5239ac876e4a45e4c779f8858ef99d/.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/95/5239ac876e4a45e4c779f8858ef99d/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BAMB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BAMB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BAMB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BAMB-N1-BDNA-1_A23KFG7LT4_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: 69450123 total, 50354 skipped (flags/unmapped)
Fragments: 34905895 total (34459853 tlen-paired, 2563 hash-paired, 410 singletons, 12850 discordant, 430219 orphans, 9304 too large [>5000 bp], 12591293 duplicates)
Reads: 74679678 total, 44765 skipped (flags/unmapped)
Fragments: 37532969 total (37070664 tlen-paired, 2530 hash-paired, 485 singletons, 8918 discordant, 450372 orphans, 9916 too large [>5000 bp], 13233724 duplicates)
Reads: 81273464 total, 47613 skipped (flags/unmapped)
Fragments: 40847343 total (40329656 tlen-paired, 3583 hash-paired, 314 singletons, 13089 discordant, 500701 orphans, 16090 too large [>5000 bp], 14780768 duplicates)
Reads: 82573073 total, 80514 skipped (flags/unmapped)
Fragments: 41722045 total (40237054 tlen-paired, 2956 hash-paired, 423 singletons, 292702 discordant, 1188910 orphans, 118901 too large [>5000 bp], 15000018 duplicates)