Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BNIR-N1-BDNA-1_A23NLN3LT4_1/1029_BNIR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BNIR-N1-BDNA-1_A23NLN3LT4_1/1029_BNIR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/9be19066df017e15dd9efbe80b9279/.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/b5/9be19066df017e15dd9efbe80b9279/.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: 1029_BNIR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNIR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNIR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNIR-N1-BDNA-1_A23NLN3LT4_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: 66989428 total, 47365 skipped (flags/unmapped)
Fragments: 33591533 total (33312294 tlen-paired, 2564 hash-paired, 281 singletons, 13158 discordant, 263236 orphans, 11257 too large [>5000 bp], 12432681 duplicates)
Reads: 72430447 total, 39188 skipped (flags/unmapped)
Fragments: 36327465 total (36036023 tlen-paired, 2221 hash-paired, 374 singletons, 9446 discordant, 279401 orphans, 8052 too large [>5000 bp], 13098091 duplicates)
Reads: 71999142 total, 42319 skipped (flags/unmapped)
Fragments: 36110072 total (35805006 tlen-paired, 2454 hash-paired, 242 singletons, 11011 discordant, 291359 orphans, 14140 too large [>5000 bp], 13425764 duplicates)
Reads: 79286468 total, 71136 skipped (flags/unmapped)
Fragments: 39861145 total (39063478 tlen-paired, 2803 hash-paired, 290 singletons, 156008 discordant, 638566 orphans, 65949 too large [>5000 bp], 14811807 duplicates)