Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_3/869_G71-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/14400ddf6c4f7a1b208f75154aad49/.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/6b/14400ddf6c4f7a1b208f75154aad49/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_3/869_G71-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
==> 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_G71-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G71-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: 102464273 total, 95483 skipped (flags/unmapped)
Fragments: 51365937 total (50902803 tlen-paired, 60008 hash-paired, 8883 singletons, 10578 discordant, 383665 orphans, 14732 too large [>5000 bp], 13462446 duplicates)
Reads: 111153141 total, 84471 skipped (flags/unmapped)
Fragments: 55738713 total (55232854 tlen-paired, 64649 hash-paired, 9549 singletons, 7514 discordant, 424147 orphans, 12470 too large [>5000 bp], 14594995 duplicates)
Reads: 111921972 total, 80666 skipped (flags/unmapped)
Fragments: 56132667 total (55594444 tlen-paired, 64692 hash-paired, 9758 singletons, 10739 discordant, 453034 orphans, 19382 too large [>5000 bp], 14614219 duplicates)
Reads: 115229901 total, 145013 skipped (flags/unmapped)
Fragments: 57978142 total (56567755 tlen-paired, 69247 hash-paired, 10094 singletons, 257164 discordant, 1073882 orphans, 106290 too large [>5000 bp], 15086147 duplicates)