Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3fe3a44b53f2053f97a945b7611f8e/.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/bb/3fe3a44b53f2053f97a945b7611f8e/.command.run
  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_1/869_VH9-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  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_1/869_VH9-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_VH9-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-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: 109429129 total, 85495 skipped (flags/unmapped)
Fragments: 54844961 total (54430261 tlen-paired, 47399 hash-paired, 8385 singletons, 9625 discordant, 349291 orphans, 5694 too large [>5000 bp], 12031701 duplicates)
Reads: 119267331 total, 82183 skipped (flags/unmapped)
Fragments: 59781446 total (59323347 tlen-paired, 50133 hash-paired, 9070 singletons, 7188 discordant, 391708 orphans, 11517 too large [>5000 bp], 13123561 duplicates)
Reads: 120933733 total, 85192 skipped (flags/unmapped)
Fragments: 60612233 total (60135409 tlen-paired, 52962 hash-paired, 9313 singletons, 9851 discordant, 404698 orphans, 19043 too large [>5000 bp], 13216314 duplicates)
Reads: 122881637 total, 154136 skipped (flags/unmapped)
Fragments: 61760073 total (60488322 tlen-paired, 55100 hash-paired, 9319 singletons, 233728 discordant, 973604 orphans, 95139 too large [>5000 bp], 13470998 duplicates)