Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/d1dcd02b2a8c2176bb8cd8afcf9764/.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/00/d1dcd02b2a8c2176bb8cd8afcf9764/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> 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: 1241_BSFD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSFD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSFD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSFD-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: 19001779 total, 20725 skipped (flags/unmapped)
Fragments: 9713713 total (9258680 tlen-paired, 1447 hash-paired, 110 singletons, 1184 discordant, 452292 orphans, 3015 too large [>5000 bp], 4414876 duplicates)
Reads: 20396401 total, 19544 skipped (flags/unmapped)
Fragments: 10441298 total (9928980 tlen-paired, 884 hash-paired, 127 singletons, 1039 discordant, 510268 orphans, 2328 too large [>5000 bp], 4645420 duplicates)
Reads: 20579318 total, 18424 skipped (flags/unmapped)
Fragments: 10526963 total (10023380 tlen-paired, 1089 hash-paired, 72 singletons, 1374 discordant, 501048 orphans, 4044 too large [>5000 bp], 4879692 duplicates)
Reads: 24606512 total, 40956 skipped (flags/unmapped)
Fragments: 12851945 total (11020438 tlen-paired, 1656 hash-paired, 162 singletons, 386255 discordant, 1443434 orphans, 152631 too large [>5000 bp], 5543814 duplicates)