Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3DY-N1-BDNA-1_A23KFG7LT4_1/1136_3DY-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/aca95aaeb46490f61e471cf834ee89/.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/98/aca95aaeb46490f61e471cf834ee89/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3DY-N1-BDNA-1_A23KFG7LT4_1/1136_3DY-N1-BDNA-1_A23KFG7LT4_1.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: 1136_3DY-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DY-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DY-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DY-N1-BDNA-1_A23KFG7LT4_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: 57166440 total, 37467 skipped (flags/unmapped)
Fragments: 28666002 total (28441403 tlen-paired, 2553 hash-paired, 308 singletons, 6889 discordant, 214849 orphans, 6063 too large [>5000 bp], 9617643 duplicates)
Reads: 66170313 total, 34896 skipped (flags/unmapped)
Fragments: 33183271 total (32919067 tlen-paired, 1903 hash-paired, 226 singletons, 6574 discordant, 255501 orphans, 12301 too large [>5000 bp], 11106749 duplicates)
Reads: 60412269 total, 32148 skipped (flags/unmapped)
Fragments: 30295411 total (30066815 tlen-paired, 1455 hash-paired, 338 singletons, 4804 discordant, 221999 orphans, 5818 too large [>5000 bp], 9841202 duplicates)
Reads: 67101324 total, 55824 skipped (flags/unmapped)
Fragments: 33751759 total (33031220 tlen-paired, 2610 hash-paired, 291 singletons, 141129 discordant, 576509 orphans, 59391 too large [>5000 bp], 11326211 duplicates)