Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/567a5b648db5e1df9b7c3ab290ae14/.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/f9/567a5b648db5e1df9b7c3ab290ae14/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1/1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1/1029_BJJ7-N1-BDNA-1_A23MHW3LT4_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: 1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJJ7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJJ7-N1-BDNA-1_A23MHW3LT4_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: 72785413 total, 56046 skipped (flags/unmapped)
Fragments: 36594199 total (36097138 tlen-paired, 2894 hash-paired, 438 singletons, 13234 discordant, 480495 orphans, 10951 too large [>5000 bp], 12771873 duplicates)
Reads: 76530814 total, 47510 skipped (flags/unmapped)
Fragments: 38480998 total (37971388 tlen-paired, 2378 hash-paired, 467 singletons, 9260 discordant, 497505 orphans, 9640 too large [>5000 bp], 13079231 duplicates)
Reads: 83603308 total, 52859 skipped (flags/unmapped)
Fragments: 42041848 total (41465078 tlen-paired, 3575 hash-paired, 351 singletons, 12932 discordant, 559912 orphans, 13508 too large [>5000 bp], 14651190 duplicates)
Reads: 85421779 total, 84414 skipped (flags/unmapped)
Fragments: 43192424 total (41544359 tlen-paired, 3521 hash-paired, 488 singletons, 322599 discordant, 1321457 orphans, 137231 too large [>5000 bp], 15017681 duplicates)