Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/2fdd846510ae226531dbe4caa73bb9/.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/a3/2fdd846510ae226531dbe4caa73bb9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_VY8-N1-BDNA-1_A23TNVNLT4_1/1241_VY8-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/1241_VY8-N1-BDNA-1_A23TNVNLT4_1/1241_VY8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_VY8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_VY8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_VY8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_VY8-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: 94927999 total, 63400 skipped (flags/unmapped)
Fragments: 47632659 total (47193868 tlen-paired, 3970 hash-paired, 545 singletons, 14132 discordant, 420144 orphans, 9985 too large [>5000 bp], 19061371 duplicates)
Reads: 102142650 total, 55916 skipped (flags/unmapped)
Fragments: 51258353 total (50790653 tlen-paired, 3417 hash-paired, 636 singletons, 9453 discordant, 454194 orphans, 12429 too large [>5000 bp], 20116804 duplicates)
Reads: 111107396 total, 60593 skipped (flags/unmapped)
Fragments: 55759203 total (55225917 tlen-paired, 5155 hash-paired, 460 singletons, 13966 discordant, 513705 orphans, 21281 too large [>5000 bp], 22401929 duplicates)
Reads: 113502393 total, 109368 skipped (flags/unmapped)
Fragments: 57162468 total (55714202 tlen-paired, 3536 hash-paired, 544 singletons, 287955 discordant, 1156231 orphans, 112432 too large [>5000 bp], 22873219 duplicates)