Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7IK-N1-BDNA-1_B23KFG5LT4_1/1136_7IK-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/5574b03c1f91706c03d2da2637bd3d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7IK-N1-BDNA-1_B23KFG5LT4_1/1136_7IK-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/73/5574b03c1f91706c03d2da2637bd3d/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7IK-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7IK-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7IK-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_7IK-N1-BDNA-1_B23KFG5LT4_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: 93959332 total, 68930 skipped (flags/unmapped)
Fragments: 47106417 total (46734322 tlen-paired, 2886 hash-paired, 371 singletons, 19863 discordant, 348975 orphans, 13457 too large [>5000 bp], 21387468 duplicates)
Reads: 101614767 total, 61264 skipped (flags/unmapped)
Fragments: 50949368 total (50560701 tlen-paired, 3861 hash-paired, 525 singletons, 14065 discordant, 370216 orphans, 12754 too large [>5000 bp], 22637865 duplicates)
Reads: 102435406 total, 61693 skipped (flags/unmapped)
Fragments: 51370241 total (50943330 tlen-paired, 3771 hash-paired, 331 singletons, 17381 discordant, 405428 orphans, 19495 too large [>5000 bp], 23476682 duplicates)
Reads: 113310675 total, 100611 skipped (flags/unmapped)
Fragments: 56933119 total (55913804 tlen-paired, 2645 hash-paired, 427 singletons, 199428 discordant, 816815 orphans, 80534 too large [>5000 bp], 26048415 duplicates)