Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_B1-N1-BDNA-1_A23TNVNLT4_1/1267_B1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/747a508dc5894f1b11ef49631d84eb/.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/53/747a508dc5894f1b11ef49631d84eb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_B1-N1-BDNA-1_A23TNVNLT4_1/1267_B1-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: 1267_B1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_B1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_B1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_B1-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: 93086875 total, 68057 skipped (flags/unmapped)
Fragments: 46638929 total (46338161 tlen-paired, 4855 hash-paired, 469 singletons, 16119 discordant, 279325 orphans, 10377 too large [>5000 bp], 17281986 duplicates)
Reads: 99407821 total, 52270 skipped (flags/unmapped)
Fragments: 49810420 total (49511010 tlen-paired, 4467 hash-paired, 404 singletons, 11444 discordant, 283095 orphans, 9105 too large [>5000 bp], 18289561 duplicates)
Reads: 108690339 total, 58081 skipped (flags/unmapped)
Fragments: 54465399 total (54119587 tlen-paired, 6526 hash-paired, 370 singletons, 16696 discordant, 322220 orphans, 12025 too large [>5000 bp], 20359472 duplicates)
Reads: 109869734 total, 106917 skipped (flags/unmapped)
Fragments: 55140690 total (54347952 tlen-paired, 4503 hash-paired, 445 singletons, 149292 discordant, 638498 orphans, 60190 too large [>5000 bp], 20626236 duplicates)