Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BBKM-N1-BDNA-1_A23TNVNLT4_1/1241_BBKM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/2fa5894bc0e59f77d28d27e3a4184b/.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/ba/2fa5894bc0e59f77d28d27e3a4184b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BBKM-N1-BDNA-1_A23TNVNLT4_1/1241_BBKM-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_BBKM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BBKM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BBKM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BBKM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 32436023 total, 34376 skipped (flags/unmapped)
Fragments: 16605218 total (15781636 tlen-paired, 2048 hash-paired, 260 singletons, 3191 discordant, 818083 orphans, 4777 too large [>5000 bp], 7962127 duplicates)
Reads: 34886961 total, 32155 skipped (flags/unmapped)
Fragments: 17871900 total (16956950 tlen-paired, 2151 hash-paired, 134 singletons, 3151 discordant, 909514 orphans, 10327 too large [>5000 bp], 8763419 duplicates)
Reads: 34089204 total, 33057 skipped (flags/unmapped)
Fragments: 17470363 total (16571716 tlen-paired, 1726 hash-paired, 245 singletons, 2286 discordant, 894390 orphans, 5028 too large [>5000 bp], 8263748 duplicates)
Reads: 42080943 total, 67792 skipped (flags/unmapped)
Fragments: 22016267 total (18752752 tlen-paired, 2113 hash-paired, 276 singletons, 692285 discordant, 2568841 orphans, 274867 too large [>5000 bp], 10068452 duplicates)