Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_bZH-N1-BDNA-1_B23L5TMLT4_1/659_bZH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/998aa9d564c6c3f1fbb2ea7494ec65/.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/f1/998aa9d564c6c3f1fbb2ea7494ec65/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_bZH-N1-BDNA-1_B23L5TMLT4_1/659_bZH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_bZH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 659_bZH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bZH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_bZH-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: 79059679 total, 66511 skipped (flags/unmapped)
Fragments: 39655941 total (39291832 tlen-paired, 4778 hash-paired, 405 singletons, 15403 discordant, 343523 orphans, 12607 too large [>5000 bp], 13928945 duplicates)
Reads: 83885306 total, 57685 skipped (flags/unmapped)
Fragments: 42086329 total (41684300 tlen-paired, 8177 hash-paired, 445 singletons, 13311 discordant, 380096 orphans, 17752 too large [>5000 bp], 14847415 duplicates)
Reads: 85164527 total, 55377 skipped (flags/unmapped)
Fragments: 42718857 total (42349728 tlen-paired, 4478 hash-paired, 497 singletons, 10837 discordant, 353317 orphans, 12625 too large [>5000 bp], 14723794 duplicates)
Reads: 92108770 total, 97763 skipped (flags/unmapped)
Fragments: 46339526 total (45296054 tlen-paired, 4052 hash-paired, 435 singletons, 202919 discordant, 836066 orphans, 84228 too large [>5000 bp], 16316748 duplicates)