Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_B2C9-N1-BDNA-1_A23TY32LT4_1/1241_B2C9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_B2C9-N1-BDNA-1_A23TY32LT4_1/1241_B2C9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/17add3aa087f8f7a293b006ca500c7/.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/87/17add3aa087f8f7a293b006ca500c7/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_B2C9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1241_B2C9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

The index file is older than the data file: 1241_B2C9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_B2C9-N1-BDNA-1_A23TY32LT4_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: 72065772 total, 52401 skipped (flags/unmapped)
Fragments: 36140655 total (35842092 tlen-paired, 2900 hash-paired, 346 singletons, 10820 discordant, 284497 orphans, 8452 too large [>5000 bp], 14622851 duplicates)
Reads: 77470143 total, 45096 skipped (flags/unmapped)
Fragments: 38855467 total (38541142 tlen-paired, 3513 hash-paired, 430 singletons, 7771 discordant, 302611 orphans, 8577 too large [>5000 bp], 15485460 duplicates)
Reads: 85340442 total, 47754 skipped (flags/unmapped)
Fragments: 42804101 total (42442397 tlen-paired, 2768 hash-paired, 293 singletons, 10928 discordant, 347715 orphans, 16247 too large [>5000 bp], 17379881 duplicates)
Reads: 86084505 total, 89161 skipped (flags/unmapped)
Fragments: 43300923 total (42359492 tlen-paired, 3167 hash-paired, 369 singletons, 184542 discordant, 753353 orphans, 73610 too large [>5000 bp], 17528409 duplicates)