Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_56Y-N1-BDNA-1_A23MHW3LT4_1/1029_56Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/d8cf4d2a91aa223107bc018d24e4d4/.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/17/d8cf4d2a91aa223107bc018d24e4d4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_56Y-N1-BDNA-1_A23MHW3LT4_1/1029_56Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_56Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_56Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_56Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_56Y-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: 52535507 total, 41419 skipped (flags/unmapped)
Fragments: 26418025 total (26049921 tlen-paired, 2216 hash-paired, 343 singletons, 9654 discordant, 355891 orphans, 7136 too large [>5000 bp], 8927561 duplicates)
Reads: 62097612 total, 61511 skipped (flags/unmapped)
Fragments: 31408548 total (30185438 tlen-paired, 2736 hash-paired, 342 singletons, 240111 discordant, 979921 orphans, 99634 too large [>5000 bp], 10544936 duplicates)
Reads: 55560639 total, 36066 skipped (flags/unmapped)
Fragments: 27937320 total (27563264 tlen-paired, 2182 hash-paired, 389 singletons, 6539 discordant, 364946 orphans, 7634 too large [>5000 bp], 9210830 duplicates)
Reads: 61080227 total, 40408 skipped (flags/unmapped)
Fragments: 30714161 total (30277110 tlen-paired, 3962 hash-paired, 323 singletons, 10050 discordant, 422716 orphans, 17268 too large [>5000 bp], 10359247 duplicates)