Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1029_MB8-N1-BDNA-1_A23H3W5LT3_1/1029_MB8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/873d1395b808df960db2a6e545e829/.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/90/873d1395b808df960db2a6e545e829/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1029_MB8-N1-BDNA-1_A23H3W5LT3_1/1029_MB8-N1-BDNA-1_A23H3W5LT3_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: 1029_MB8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MB8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MB8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MB8-N1-BDNA-1_A23H3W5LT3_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: 90902891 total, 77551 skipped (flags/unmapped)
Fragments: 45557161 total (45213990 tlen-paired, 17185 hash-paired, 5993 singletons, 11002 discordant, 308991 orphans, 13001 too large [>5000 bp], 9490708 duplicates)
Reads: 91384403 total, 65823 skipped (flags/unmapped)
Fragments: 45812601 total (45439939 tlen-paired, 17976 hash-paired, 6027 singletons, 9702 discordant, 338957 orphans, 19181 too large [>5000 bp], 9501028 duplicates)
Reads: 100082460 total, 64662 skipped (flags/unmapped)
Fragments: 50174770 total (49798940 tlen-paired, 16701 hash-paired, 6314 singletons, 8307 discordant, 344508 orphans, 9540 too large [>5000 bp], 10467573 duplicates)
Reads: 101790627 total, 119156 skipped (flags/unmapped)
Fragments: 51161400 total (50134950 tlen-paired, 20294 hash-paired, 6592 singletons, 194985 discordant, 804579 orphans, 79921 too large [>5000 bp], 10589517 duplicates)