Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0FX-N1-BDNA-1_A23MHW3LT4_1/1136_0FX-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/ec852bcfcfa7df167eaf46a1324774/.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/b3/ec852bcfcfa7df167eaf46a1324774/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0FX-N1-BDNA-1_A23MHW3LT4_1/1136_0FX-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> 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: 1136_0FX-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0FX-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0FX-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0FX-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: 103104099 total, 66651 skipped (flags/unmapped)
Fragments: 51850938 total (51141513 tlen-paired, 3187 hash-paired, 679 singletons, 12416 discordant, 693143 orphans, 14697 too large [>5000 bp], 19973597 duplicates)
Reads: 98821603 total, 80709 skipped (flags/unmapped)
Fragments: 49691365 total (48995997 tlen-paired, 5260 hash-paired, 543 singletons, 18840 discordant, 670725 orphans, 14716 too large [>5000 bp], 19599315 duplicates)
Reads: 113198695 total, 78642 skipped (flags/unmapped)
Fragments: 56922708 total (56103404 tlen-paired, 6907 hash-paired, 603 singletons, 17966 discordant, 793828 orphans, 34534 too large [>5000 bp], 22451280 duplicates)
Reads: 115206160 total, 118307 skipped (flags/unmapped)
Fragments: 58281592 total (55970812 tlen-paired, 3294 hash-paired, 604 singletons, 454819 discordant, 1852063 orphans, 188668 too large [>5000 bp], 22801245 duplicates)