Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/80b9201fd85152a7bcd73138d52cae/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BQ-N1-BDNA-1_A23TNVNLT4_1/1267_BQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BQ-N1-BDNA-1_A23TNVNLT4_1/1267_BQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/16/80b9201fd85152a7bcd73138d52cae/.command.run
==> 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: 1267_BQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BQ-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: 71817806 total, 47990 skipped (flags/unmapped)
Fragments: 35992622 total (35743767 tlen-paired, 2588 hash-paired, 402 singletons, 13651 discordant, 232214 orphans, 8594 too large [>5000 bp], 12476159 duplicates)
Reads: 76516746 total, 42062 skipped (flags/unmapped)
Fragments: 38347615 total (38097576 tlen-paired, 3266 hash-paired, 352 singletons, 9225 discordant, 237196 orphans, 8501 too large [>5000 bp], 13037991 duplicates)
Reads: 83798624 total, 45119 skipped (flags/unmapped)
Fragments: 41998891 total (41702923 tlen-paired, 4196 hash-paired, 327 singletons, 13827 discordant, 277618 orphans, 16834 too large [>5000 bp], 14588695 duplicates)
Reads: 84684645 total, 76638 skipped (flags/unmapped)
Fragments: 42519165 total (41858587 tlen-paired, 2876 hash-paired, 368 singletons, 125381 discordant, 531953 orphans, 50999 too large [>5000 bp], 14783956 duplicates)