Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_1/869_CXK-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0b75551f8743e695c45e8ce453eac9/.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/b0/0b75551f8743e695c45e8ce453eac9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_1/869_CXK-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
==> 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_CXK-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_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: 76701050 total, 62911 skipped (flags/unmapped)
Fragments: 38480097 total (38114368 tlen-paired, 26950 hash-paired, 5685 singletons, 7716 discordant, 325378 orphans, 4504 too large [>5000 bp], 7087912 duplicates)
Reads: 77342464 total, 61150 skipped (flags/unmapped)
Fragments: 38804140 total (38422046 tlen-paired, 28061 hash-paired, 5728 singletons, 6685 discordant, 341620 orphans, 10191 too large [>5000 bp], 7143514 duplicates)
Reads: 84619428 total, 62005 skipped (flags/unmapped)
Fragments: 42457591 total (42045744 tlen-paired, 28764 hash-paired, 6200 singletons, 5908 discordant, 370975 orphans, 9708 too large [>5000 bp], 7846542 duplicates)
Reads: 86403329 total, 110887 skipped (flags/unmapped)
Fragments: 43516820 total (42337294 tlen-paired, 29372 hash-paired, 6229 singletons, 228322 discordant, 915603 orphans, 90317 too large [>5000 bp], 7962956 duplicates)