Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/1b800cae461b2cc9b0888b62797ddd/.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/63/1b800cae461b2cc9b0888b62797ddd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_4UU-N1-BDNA-1_A23NLN3LT4_1/1136_4UU-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_4UU-N1-BDNA-1_A23NLN3LT4_1/1136_4UU-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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_4UU-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4UU-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4UU-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4UU-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: 79161662 total, 53005 skipped (flags/unmapped)
Fragments: 39662872 total (39407165 tlen-paired, 2582 hash-paired, 394 singletons, 15348 discordant, 237383 orphans, 10345 too large [>5000 bp], 12846275 duplicates)
Reads: 84805358 total, 49824 skipped (flags/unmapped)
Fragments: 42498369 total (42195416 tlen-paired, 4451 hash-paired, 353 singletons, 13696 discordant, 284453 orphans, 21801 too large [>5000 bp], 13861316 duplicates)
Reads: 85249023 total, 46018 skipped (flags/unmapped)
Fragments: 42713884 total (42456558 tlen-paired, 2968 hash-paired, 468 singletons, 10397 discordant, 243493 orphans, 9599 too large [>5000 bp], 13571530 duplicates)
Reads: 93386496 total, 81943 skipped (flags/unmapped)
Fragments: 46860546 total (46221361 tlen-paired, 1983 hash-paired, 342 singletons, 120815 discordant, 516045 orphans, 49924 too large [>5000 bp], 15338590 duplicates)