Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_01U-N1-BDNA-1_A23KFG7LT4_1/1136_01U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/2aa6ba00902de72be796dcb831930c/.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/09/2aa6ba00902de72be796dcb831930c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_01U-N1-BDNA-1_A23KFG7LT4_1/1136_01U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] Count mode: frac
The index file is older than the data file: 1136_01U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01U-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: 68892134 total, 43263 skipped (flags/unmapped)
Fragments: 34516712 total (34307636 tlen-paired, 2842 hash-paired, 380 singletons, 9309 discordant, 196545 orphans, 6186 too large [>5000 bp], 11910182 duplicates)
Reads: 80277677 total, 41463 skipped (flags/unmapped)
Fragments: 40224617 total (39961142 tlen-paired, 4414 hash-paired, 279 singletons, 9455 discordant, 249327 orphans, 18293 too large [>5000 bp], 13880093 duplicates)
Reads: 73841623 total, 38323 skipped (flags/unmapped)
Fragments: 36996983 total (36781508 tlen-paired, 2681 hash-paired, 379 singletons, 6434 discordant, 205981 orphans, 7847 too large [>5000 bp], 12400947 duplicates)
Reads: 81326314 total, 69781 skipped (flags/unmapped)
Fragments: 40822129 total (40217154 tlen-paired, 3088 hash-paired, 305 singletons, 115718 discordant, 485864 orphans, 49222 too large [>5000 bp], 14125035 duplicates)