Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_TBA-N1-BDNA-1_A23TNVNLT4_1/1241_TBA-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/17c33581a116f34b64d1ba82dabaa9/.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/5a/17c33581a116f34b64d1ba82dabaa9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_TBA-N1-BDNA-1_A23TNVNLT4_1/1241_TBA-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_TBA-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TBA-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TBA-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TBA-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: 87651246 total, 58026 skipped (flags/unmapped)
Fragments: 43978863 total (43580106 tlen-paired, 2909 hash-paired, 368 singletons, 12204 discordant, 383276 orphans, 9569 too large [>5000 bp], 17036562 duplicates)
Reads: 93597787 total, 50614 skipped (flags/unmapped)
Fragments: 46973326 total (46544338 tlen-paired, 2992 hash-paired, 521 singletons, 8777 discordant, 416698 orphans, 8870 too large [>5000 bp], 17846942 duplicates)
Reads: 103880369 total, 53394 skipped (flags/unmapped)
Fragments: 52131386 total (51657117 tlen-paired, 4564 hash-paired, 379 singletons, 12310 discordant, 457016 orphans, 10799 too large [>5000 bp], 20340495 duplicates)
Reads: 105883928 total, 101985 skipped (flags/unmapped)
Fragments: 53321409 total (51975726 tlen-paired, 3103 hash-paired, 447 singletons, 271003 discordant, 1071130 orphans, 105351 too large [>5000 bp], 20699589 duplicates)