Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0BP-N1-BDNA-1_A23MHW3LT4_1/1136_0BP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/daf0485a66047e5f4c25c3351f8ec6/.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/92/daf0485a66047e5f4c25c3351f8ec6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0BP-N1-BDNA-1_A23MHW3LT4_1/1136_0BP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_0BP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0BP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_0BP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 

The index file is older than the data file: 1136_0BP-N1-BDNA-1_A23MHW3LT4_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: 54229224 total, 44176 skipped (flags/unmapped)
Fragments: 27261547 total (26889604 tlen-paired, 2584 hash-paired, 340 singletons, 12469 discordant, 356550 orphans, 9422 too large [>5000 bp], 8568489 duplicates)
Reads: 57017951 total, 38280 skipped (flags/unmapped)
Fragments: 28670534 total (28266653 tlen-paired, 2522 hash-paired, 335 singletons, 10858 discordant, 390166 orphans, 14552 too large [>5000 bp], 9023760 duplicates)
Reads: 58381039 total, 36478 skipped (flags/unmapped)
Fragments: 29349452 total (28966988 tlen-paired, 2118 hash-paired, 404 singletons, 8733 discordant, 371209 orphans, 8635 too large [>5000 bp], 8980102 duplicates)
Reads: 63684836 total, 63250 skipped (flags/unmapped)
Fragments: 32176217 total (31018174 tlen-paired, 2155 hash-paired, 335 singletons, 231034 discordant, 924519 orphans, 97003 too large [>5000 bp], 10118123 duplicates)