Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHQA-N1-BDNA-1_B23L5TMLT4_1/1029_BHQA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/fad9695c49da0cfd083f5d0054db10/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHQA-N1-BDNA-1_B23L5TMLT4_1/1029_BHQA-N1-BDNA-1_B23L5TMLT4_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/39/fad9695c49da0cfd083f5d0054db10/.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_BHQA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHQA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHQA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHQA-N1-BDNA-1_B23L5TMLT4_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: 71711704 total, 54794 skipped (flags/unmapped)
Fragments: 35987250 total (35632585 tlen-paired, 3084 hash-paired, 457 singletons, 13751 discordant, 337373 orphans, 10120 too large [>5000 bp], 13203738 duplicates)
Reads: 76453358 total, 45959 skipped (flags/unmapped)
Fragments: 38369362 total (38007037 tlen-paired, 3234 hash-paired, 482 singletons, 9286 discordant, 349323 orphans, 9240 too large [>5000 bp], 13860656 duplicates)
Reads: 84233716 total, 85291 skipped (flags/unmapped)
Fragments: 42419390 total (41346141 tlen-paired, 4270 hash-paired, 469 singletons, 205466 discordant, 863044 orphans, 86579 too large [>5000 bp], 15546442 duplicates)
Reads: 83547736 total, 51341 skipped (flags/unmapped)
Fragments: 41931789 total (41517775 tlen-paired, 4423 hash-paired, 392 singletons, 13826 discordant, 395373 orphans, 14291 too large [>5000 bp], 15404186 duplicates)