Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/09233b135c28e2370c53f0130698d0/.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/44/09233b135c28e2370c53f0130698d0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BTQN-N1-BDNA-1_A23TNVNLT4_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: 1241_BTQN-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BTQN-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BTQN-N1-BDNA-1_A23TNVNLT4_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: 102428327 total, 61728 skipped (flags/unmapped)
Fragments: 51325184 total (51004022 tlen-paired, 3519 hash-paired, 450 singletons, 13926 discordant, 303267 orphans, 9974 too large [>5000 bp], 17383249 duplicates)
Reads: 111122500 total, 53166 skipped (flags/unmapped)
Fragments: 55683868 total (55353952 tlen-paired, 3469 hash-paired, 583 singletons, 9771 discordant, 316093 orphans, 9137 too large [>5000 bp], 18570297 duplicates)
Reads: 119820300 total, 62650 skipped (flags/unmapped)
Fragments: 60039213 total (59642998 tlen-paired, 5831 hash-paired, 383 singletons, 14358 discordant, 375643 orphans, 27625 too large [>5000 bp], 20476973 duplicates)
Reads: 121333447 total, 100827 skipped (flags/unmapped)
Fragments: 60919224 total (59982093 tlen-paired, 3536 hash-paired, 506 singletons, 179475 discordant, 753614 orphans, 74146 too large [>5000 bp], 20823348 duplicates)