Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1MV-N1-BDNA-1_A23MHW3LT4_1/1136_1MV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/1a46a0e9bdf0388f68b2f18bd6eee3/.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/a6/1a46a0e9bdf0388f68b2f18bd6eee3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1MV-N1-BDNA-1_A23MHW3LT4_1/1136_1MV-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_1MV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MV-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: 92795540 total, 57247 skipped (flags/unmapped)
Fragments: 46608590 total (46086193 tlen-paired, 3629 hash-paired, 577 singletons, 14641 discordant, 503550 orphans, 12620 too large [>5000 bp], 16263994 duplicates)
Reads: 87302810 total, 65692 skipped (flags/unmapped)
Fragments: 43856462 total (43333082 tlen-paired, 3298 hash-paired, 563 singletons, 22068 discordant, 497451 orphans, 11104 too large [>5000 bp], 15565252 duplicates)
Reads: 101223262 total, 60736 skipped (flags/unmapped)
Fragments: 50847861 total (50253803 tlen-paired, 4822 hash-paired, 454 singletons, 21974 discordant, 566808 orphans, 17033 too large [>5000 bp], 18216582 duplicates)
Reads: 102481558 total, 101194 skipped (flags/unmapped)
Fragments: 51684479 total (50142716 tlen-paired, 4667 hash-paired, 537 singletons, 295442 discordant, 1241117 orphans, 126530 too large [>5000 bp], 18472530 duplicates)