Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_Q74-N1-BDNA-1_B2377KTLT3_3/869_Q74-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/121fe2170c744dca28148463a237c8/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_Q74-N1-BDNA-1_B2377KTLT3_3/869_Q74-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/121fe2170c744dca28148463a237c8/.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_Q74-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_Q74-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_Q74-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_Q74-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: 65360983 total, 65020 skipped (flags/unmapped)
Fragments: 32766694 total (32475141 tlen-paired, 27981 hash-paired, 4911 singletons, 6413 discordant, 252248 orphans, 9867 too large [>5000 bp], 6346415 duplicates)
Reads: 73588456 total, 93113 skipped (flags/unmapped)
Fragments: 37040570 total (36113546 tlen-paired, 29459 hash-paired, 5429 singletons, 171206 discordant, 720930 orphans, 70281 too large [>5000 bp], 7109548 duplicates)
Reads: 72269687 total, 50403 skipped (flags/unmapped)
Fragments: 36247489 total (35911206 tlen-paired, 29044 hash-paired, 5236 singletons, 6251 discordant, 295752 orphans, 12647 too large [>5000 bp], 6983918 duplicates)
Reads: 72686645 total, 50189 skipped (flags/unmapped)
Fragments: 36454572 total (36131658 tlen-paired, 28895 hash-paired, 5230 singletons, 4671 discordant, 284118 orphans, 8330 too large [>5000 bp], 7092717 duplicates)