Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BABG-N1-BDNA-1_A23NLN3LT4_1/1029_BABG-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/764c3ddab7d07bf54a93118e1e84aa/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BABG-N1-BDNA-1_A23NLN3LT4_1/1029_BABG-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/47/764c3ddab7d07bf54a93118e1e84aa/.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_BABG-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BABG-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_BABG-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BABG-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: 91941297 total, 64224 skipped (flags/unmapped)
Fragments: 46066258 total (45767481 tlen-paired, 4227 hash-paired, 438 singletons, 15561 discordant, 278551 orphans, 11773 too large [>5000 bp], 16183804 duplicates)
Reads: 99069582 total, 56035 skipped (flags/unmapped)
Fragments: 49640545 total (49337428 tlen-paired, 2367 hash-paired, 521 singletons, 11229 discordant, 289000 orphans, 10989 too large [>5000 bp], 17098082 duplicates)
Reads: 98363394 total, 60203 skipped (flags/unmapped)
Fragments: 49286511 total (48946141 tlen-paired, 4065 hash-paired, 384 singletons, 13322 discordant, 322599 orphans, 26576 too large [>5000 bp], 17460327 duplicates)
Reads: 108954482 total, 94783 skipped (flags/unmapped)
Fragments: 54683045 total (53894442 tlen-paired, 2160 hash-paired, 393 singletons, 154070 discordant, 631980 orphans, 62991 too large [>5000 bp], 19371301 duplicates)