Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_5KP-N1-BDNA-1_A23KFG7LT4_1/1029_5KP-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_5KP-N1-BDNA-1_A23KFG7LT4_1/1029_5KP-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/345765ad77aef525cfac4bd55869be/.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/1c/345765ad77aef525cfac4bd55869be/.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_5KP-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5KP-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5KP-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5KP-N1-BDNA-1_A23KFG7LT4_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: 63444524 total, 47655 skipped (flags/unmapped)
Fragments: 31812860 total (31562467 tlen-paired, 3036 hash-paired, 303 singletons, 6102 discordant, 240952 orphans, 6202 too large [>5000 bp], 11778034 duplicates)
Reads: 68816998 total, 43748 skipped (flags/unmapped)
Fragments: 34519378 total (34205015 tlen-paired, 2432 hash-paired, 239 singletons, 6323 discordant, 305369 orphans, 20051 too large [>5000 bp], 12768690 duplicates)
Reads: 71543742 total, 42455 skipped (flags/unmapped)
Fragments: 35891716 total (35586520 tlen-paired, 2446 hash-paired, 399 singletons, 5261 discordant, 297090 orphans, 7672 too large [>5000 bp], 13052959 duplicates)
Reads: 75474907 total, 80054 skipped (flags/unmapped)
Fragments: 37985524 total (37095405 tlen-paired, 2825 hash-paired, 390 singletons, 182853 discordant, 704051 orphans, 64123 too large [>5000 bp], 13987358 duplicates)