Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_eK7-N1-BDNA-1_A23TY32LT4_1/659_eK7-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_eK7-N1-BDNA-1_A23TY32LT4_1/659_eK7-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b05ca128c2fea44923f4b77cb66546/.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/de/b05ca128c2fea44923f4b77cb66546/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_eK7-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_eK7-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eK7-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eK7-N1-BDNA-1_A23TY32LT4_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: 118279078 total, 90911 skipped (flags/unmapped)
Fragments: 59308548 total (58820089 tlen-paired, 5211 hash-paired, 533 singletons, 24813 discordant, 457902 orphans, 14753 too large [>5000 bp], 24872157 duplicates)
Reads: 128112105 total, 78110 skipped (flags/unmapped)
Fragments: 64240749 total (63737061 tlen-paired, 6095 hash-paired, 666 singletons, 17646 discordant, 479281 orphans, 16222 too large [>5000 bp], 26664506 duplicates)
Reads: 127464930 total, 83327 skipped (flags/unmapped)
Fragments: 63920633 total (63375112 tlen-paired, 6796 hash-paired, 446 singletons, 21488 discordant, 516791 orphans, 28787 too large [>5000 bp], 27126590 duplicates)
Reads: 140899584 total, 141652 skipped (flags/unmapped)
Fragments: 70809883 total (69466989 tlen-paired, 4849 hash-paired, 508 singletons, 262813 discordant, 1074724 orphans, 106699 too large [>5000 bp], 30079028 duplicates)