Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e53c7db9f40086118d6c117912eeaf/.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/9b/e53c7db9f40086118d6c117912eeaf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> 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_BP9P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BP9P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BP9P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BP9P-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: 79784516 total, 51023 skipped (flags/unmapped)
Fragments: 40042471 total (39655635 tlen-paired, 3281 hash-paired, 325 singletons, 12784 discordant, 370446 orphans, 9661 too large [>5000 bp], 14411004 duplicates)
Reads: 85800289 total, 44521 skipped (flags/unmapped)
Fragments: 43067884 total (42658884 tlen-paired, 1818 hash-paired, 461 singletons, 9160 discordant, 397561 orphans, 9011 too large [>5000 bp], 15202811 duplicates)
Reads: 93673313 total, 47268 skipped (flags/unmapped)
Fragments: 47018961 total (46560580 tlen-paired, 4038 hash-paired, 350 singletons, 13556 discordant, 440437 orphans, 14455 too large [>5000 bp], 17028436 duplicates)
Reads: 95549275 total, 81839 skipped (flags/unmapped)
Fragments: 48136810 total (46883813 tlen-paired, 1362 hash-paired, 383 singletons, 247739 discordant, 1003513 orphans, 98856 too large [>5000 bp], 17376886 duplicates)