Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_624-N1-BDNA-1_A23NLN3LT4_1/1136_624-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/a8632d0dedd350bdb58e6daad75666/.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/03/a8632d0dedd350bdb58e6daad75666/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_624-N1-BDNA-1_A23NLN3LT4_1/1136_624-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_624-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_624-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_624-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_624-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: 99155218 total, 71377 skipped (flags/unmapped)
Fragments: 49689902 total (49345648 tlen-paired, 3829 hash-paired, 516 singletons, 20126 discordant, 319783 orphans, 12168 too large [>5000 bp], 19009734 duplicates)
Reads: 105848515 total, 64260 skipped (flags/unmapped)
Fragments: 53042932 total (52698694 tlen-paired, 3411 hash-paired, 546 singletons, 13920 discordant, 326361 orphans, 12649 too large [>5000 bp], 19970945 duplicates)
Reads: 106394468 total, 67674 skipped (flags/unmapped)
Fragments: 53320161 total (52932820 tlen-paired, 5687 hash-paired, 394 singletons, 16934 discordant, 364326 orphans, 25596 too large [>5000 bp], 20557243 duplicates)
Reads: 117208318 total, 102547 skipped (flags/unmapped)
Fragments: 58834263 total (57967809 tlen-paired, 3788 hash-paired, 405 singletons, 165775 discordant, 696486 orphans, 67068 too large [>5000 bp], 22721083 duplicates)