Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/b93ed601407d520b9830ade713743a/.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/d9/b93ed601407d520b9830ade713743a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_JG-N1-BDNA-1_B23KGCJLT4_1/1047_JG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_JG-N1-BDNA-1_B23KGCJLT4_1/1047_JG-N1-BDNA-1_B23KGCJLT4_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: 1047_JG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JG-N1-BDNA-1_B23KGCJLT4_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: 56278157 total, 41855 skipped (flags/unmapped)
Fragments: 28199636 total (28012192 tlen-paired, 2945 hash-paired, 245 singletons, 8291 discordant, 175963 orphans, 6619 too large [>5000 bp], 10292295 duplicates)
Reads: 66084555 total, 36518 skipped (flags/unmapped)
Fragments: 33123361 total (32880396 tlen-paired, 2367 hash-paired, 248 singletons, 8445 discordant, 231905 orphans, 16734 too large [>5000 bp], 12163531 duplicates)
Reads: 59987250 total, 32846 skipped (flags/unmapped)
Fragments: 30062388 total (29870336 tlen-paired, 2331 hash-paired, 298 singletons, 5731 discordant, 183692 orphans, 6809 too large [>5000 bp], 10804193 duplicates)
Reads: 66876305 total, 59770 skipped (flags/unmapped)
Fragments: 33580939 total (33039226 tlen-paired, 2665 hash-paired, 289 singletons, 104207 discordant, 434552 orphans, 44749 too large [>5000 bp], 12322374 duplicates)