Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VH9-N1-BDNA-1_B2377KTLT3_3/869_VH9-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/26fe5be11466675f3a73de5e975a36/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VH9-N1-BDNA-1_B2377KTLT3_3/869_VH9-N1-BDNA-1_B2377KTLT3_3.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/03/26fe5be11466675f3a73de5e975a36/.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: 869_VH9-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_3.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: 64704984 total, 56319 skipped (flags/unmapped)
Fragments: 32445609 total (32152162 tlen-paired, 21388 hash-paired, 5044 singletons, 5404 discordant, 261611 orphans, 12051 too large [>5000 bp], 6112006 duplicates)
Reads: 70956155 total, 48436 skipped (flags/unmapped)
Fragments: 35600052 total (35268450 tlen-paired, 21955 hash-paired, 5268 singletons, 3954 discordant, 300425 orphans, 6654 too large [>5000 bp], 6716575 duplicates)
Reads: 72852992 total, 88564 skipped (flags/unmapped)
Fragments: 36696497 total (35708317 tlen-paired, 24900 hash-paired, 5642 singletons, 185590 discordant, 772048 orphans, 74562 too large [>5000 bp], 6818459 duplicates)
Reads: 71290893 total, 49085 skipped (flags/unmapped)
Fragments: 35767912 total (35421462 tlen-paired, 23034 hash-paired, 5436 singletons, 5424 discordant, 312556 orphans, 11988 too large [>5000 bp], 6689545 duplicates)