Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_dyZ-N1-BDNA-1_A23TY32LT4_1/659_dyZ-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_dyZ-N1-BDNA-1_A23TY32LT4_1/659_dyZ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/165691acdb59d314d1f4c9a8f23542/.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/89/165691acdb59d314d1f4c9a8f23542/.command.run
==> 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: 659_dyZ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dyZ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dyZ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_dyZ-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: 63836940 total, 39553 skipped (flags/unmapped)
Fragments: 32015641 total (31745137 tlen-paired, 3230 hash-paired, 251 singletons, 9381 discordant, 257642 orphans, 11999 too large [>5000 bp], 12181185 duplicates)
Reads: 59625589 total, 46088 skipped (flags/unmapped)
Fragments: 29898088 total (29649139 tlen-paired, 3007 hash-paired, 276 singletons, 11151 discordant, 234515 orphans, 9058 too large [>5000 bp], 11330372 duplicates)
Reads: 64328950 total, 40278 skipped (flags/unmapped)
Fragments: 32258861 total (32003270 tlen-paired, 3254 hash-paired, 327 singletons, 7967 discordant, 244043 orphans, 7660 too large [>5000 bp], 11993747 duplicates)
Reads: 70743701 total, 71639 skipped (flags/unmapped)
Fragments: 35564101 total (34851776 tlen-paired, 2940 hash-paired, 269 singletons, 141227 discordant, 567889 orphans, 56009 too large [>5000 bp], 13511096 duplicates)