Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4KD-N1-BDNA-1_B23KFG5LT4_1/1136_4KD-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4KD-N1-BDNA-1_B23KFG5LT4_1/1136_4KD-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/ae994280e670e96dc781cd4adf157a/.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/f4/ae994280e670e96dc781cd4adf157a/.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: 1136_4KD-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4KD-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4KD-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4KD-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: 64870643 total, 46951 skipped (flags/unmapped)
Fragments: 32523643 total (32268707 tlen-paired, 2148 hash-paired, 310 singletons, 13408 discordant, 239070 orphans, 7893 too large [>5000 bp], 12588331 duplicates)
Reads: 70140122 total, 44169 skipped (flags/unmapped)
Fragments: 35167957 total (34878118 tlen-paired, 2510 hash-paired, 262 singletons, 12370 discordant, 274697 orphans, 17499 too large [>5000 bp], 13673192 duplicates)
Reads: 70115170 total, 42965 skipped (flags/unmapped)
Fragments: 35151542 total (34887294 tlen-paired, 3000 hash-paired, 313 singletons, 10201 discordant, 250734 orphans, 10084 too large [>5000 bp], 13278427 duplicates)
Reads: 77536592 total, 69561 skipped (flags/unmapped)
Fragments: 38953500 total (38270157 tlen-paired, 2574 hash-paired, 326 singletons, 132776 discordant, 547667 orphans, 54012 too large [>5000 bp], 15158233 duplicates)